This page contains some example results from a previously prepared Companion annotation run. The tabs below display live data and behave exactly like an actual job result page (in fact, they are the result of an actual job that was run almost 2 years ago!). Click the tabs to see what data they contain.

 
Value
Number of annotated regions/sequences 37
Number of genes 8859
Gene density (genes/megabase) 282.53
Number of coding genes 8755
Number of genes with function 4814
Number of non-coding genes 104
Number of genes with multiple CDSs 87
Overall GC% 60.07
Coding GC% 62.9
Ajax loader 6b14238b9e8b005a1f5a629d1463bc12a8789afa83fa57897c5e886baeb4c829

These clusters have been created using OrthoMCL v1.4 based on BLASTP hits (word size: 4, e-value cutoff: 10-5) between the translated protein sequences of the target and reference genomes' protein-coding genes.

Cluster assignments as OrthoMCL 1.4 output file

Click and drag in the diagram below to pan around. Use the mouse wheel to zoom in and out. The newly annotated genome in this job is highlighted: LAET.

Ajax loader 6b14238b9e8b005a1f5a629d1463bc12a8789afa83fa57897c5e886baeb4c829

These clusters have been created using FastTree based on a multiple sequence alignment created by MAFFT (--auto --anysymbol --retree 1 --parttree) of the concatenated DNA sequences of up to 50 single-copy core genes from all organisms appearing as taxa in the tree above.

Tree drawn by Phylocanvas.

Multiple sequence alignment for this tree (FASTA)
Core genes used to build this tree

Each circle below represents a single target-reference pseudochromosome alignment. Click on the thumbnail to zoom in. Download all 37 images (ZIP)

Standard output:

N E X T F L O W  ~  version 0.16.5
Launching /nfs/users/nfs_s/ss34/annot-nf/annot.nf

C O M P A N I O N  ~  version 1.0.0
query               : /www/ss34/annot-web/public/system/dragonfly/production/2016/01/06/5lw9gaz9e6_L_aet.scaf.trunc.fasta
reference           : LmjF
reference directory : /www/ss34/ref_kinetoplastids
output directory    : /www/ss34/annot-web/public/jobs/6ce04589b9b64a49194d4701

[warm up] executor > local
[e1/6a0776] Submitted process > press_ncRNA_cms (1)
[78/a6ffa1] Submitted process > sanitize_input (1)
[0c/dd5a39] Submitted process > exonerate_empty_hints (1)
[59/7b9313] Submitted process > ratt_make_ref_embl (1)
[2b/1e2936] Submitted process > transcript_empty_hints (1)
[8a/66e09c] Submitted process > pseudogene_indexing (1)
[86/15d69a] Submitted process > make_ref_input_for_orthomcl (1)
[85/a6a16f] Submitted process > merge_hints (1)
[fc/ab2e04] Submitted process > contiguate_pseudochromosomes (1)
[2f/eaddf0] Submitted process > predict_tRNA (1)
[5c/0ca47c] Submitted process > run_snap (1)
[ed/cb69e1] Submitted process > make_distribution_seqs (1)
[65/a48eb9] Submitted process > pseudogene_last (1)
[79/1f70bd] Submitted process > run_augustus_contigs (1)
[dc/528998] Submitted process > run_ratt (1)
[de/119556] Submitted process > pseudogene_last (2)
[63/257207] Submitted process > predict_ncRNA (1)
[0b/95e8e4] Submitted process > pseudogene_last (3)
[1b/25cae6] Submitted process > pseudogene_last (4)
[b3/bcd81f] Submitted process > predict_ncRNA (2)
[46/087e66] Submitted process > run_augustus_pseudo (1)
[4d/cd280c] Submitted process > pseudogene_last (5)
[2b/638098] Submitted process > predict_ncRNA (3)
[eb/1ba617] Submitted process > predict_ncRNA (4)
[e0/c13c81] Submitted process > predict_ncRNA (5)
[ff/69a4ba] Submitted process > pseudogene_last (6)
[07/1a0451] Submitted process > blast_for_circos (1)
[94/c17b89] Submitted process > pseudogene_last (7)
[82/80c18c] Submitted process > ratt_to_gff3 (1)
[b5/af61da] Submitted process > predict_ncRNA (6)
[b8/825c5e] Submitted process > pseudogene_last (8)
[53/845c97] Submitted process > pseudogene_last (9)
[e7/13e968] Submitted process > predict_ncRNA (7)
[19/fc9b7f] Submitted process > pseudogene_last (10)
[4c/f27d16] Submitted process > predict_ncRNA (8)
[36/b092e0] Submitted process > pseudogene_last (11)
[dd/821a17] Submitted process > pseudogene_last (12)
[91/49ee28] Submitted process > pseudogene_last (13)
[12/c33108] Submitted process > merge_ncrnas (1)
[f7/dbf17a] Submitted process > merge_genemodels (1)
[d6/b083eb] Submitted process > integrate_genemodels (1)
[fb/f51f3a] Submitted process > fix_polycistrons (1)
[f5/6838aa] Submitted process > remove_exons (1)
[b4/44ab63] Submitted process > pseudogene_calling (1)
[fb/d581fc] Submitted process > merge_structural (1)
[a4/b67977] Submitted process > add_gap_features (1)
[20/140700] Submitted process > split_splice_models_at_gaps (1)
[11/1fe62f] Submitted process > add_polypeptides (1)
[58/5f0db1] Submitted process > get_proteins_for_orthomcl (1)
[a3/c58eef] Submitted process > run_pfam (2)
[d6/2dc094] Submitted process > run_pfam (1)
[d6/95d1a1] Submitted process > run_pfam (3)
[84/5e4063] Submitted process > run_pfam (4)
[03/d3c4eb] Submitted process > run_pfam (5)
[52/9cac7f] Submitted process > make_target_input_for_orthomcl (1)
[ed/9004e8] Submitted process > run_pfam (6)
[fb/02fbab] Submitted process > run_pfam (7)
[ff/f512ba] Submitted process > run_pfam (8)
[fa/ebfc88] Submitted process > run_pfam (9)
[95/e87ce0] Submitted process > run_pfam (10)
[4e/349ae2] Submitted process > run_pfam (11)
[c0/4488ed] Submitted process > blast_for_orthomcl_formatdb (1)
[5e/859ff6] Submitted process > run_pfam (12)
[64/9445d6] Submitted process > run_pfam (13)
[01/8eec10] Submitted process > run_pfam (14)
[1a/3e0c5d] Submitted process > run_pfam (15)
[11/4018f7] Submitted process > run_pfam (16)
[a4/252a95] Submitted process > run_pfam (17)
[a7/65d0c0] Submitted process > blast_for_orthomcl (2)
[a4/0bc7a7] Submitted process > blast_for_orthomcl (1)
[5b/5c19c3] Submitted process > blast_for_orthomcl (4)
[56/96f40c] Submitted process > blast_for_orthomcl (3)
[c6/dcba98] Submitted process > blast_for_orthomcl (5)
[27/b59982] Submitted process > run_pfam (18)
[2b/18c722] Submitted process > run_pfam (19)
[a0/ddc559] Submitted process > run_pfam (20)
[a0/3ed098] Submitted process > run_pfam (21)
[41/355545] Submitted process > run_pfam (22)
[23/5d26cb] Submitted process > blast_for_orthomcl (6)
[2b/349881] Submitted process > blast_for_orthomcl (7)
[bd/e6527c] Submitted process > blast_for_orthomcl (8)
[fb/2d12f7] Submitted process > blast_for_orthomcl (9)
[1a/950a29] Submitted process > blast_for_orthomcl (10)
[2a/d52c7d] Submitted process > run_pfam (23)
[95/769fc2] Submitted process > run_pfam (24)
[af/919b58] Submitted process > run_pfam (25)
[1c/96bde5] Submitted process > run_pfam (26)
[32/7363ad] Submitted process > run_pfam (27)
[75/37d961] Submitted process > blast_for_orthomcl (11)
[08/0aecfd] Submitted process > blast_for_orthomcl (12)
[5d/f9691b] Submitted process > blast_for_orthomcl (13)
[aa/a59f71] Submitted process > blast_for_orthomcl (14)
[f7/9f1111] Submitted process > blast_for_orthomcl (15)
[28/d2db0a] Submitted process > run_pfam (28)
[bd/f9c7bb] Submitted process > run_pfam (29)
[1e/2ff40a] Submitted process > run_pfam (30)
[82/2d5f1d] Submitted process > run_pfam (31)
[05/5b667d] Submitted process > run_pfam (32)
[8b/1c26bb] Submitted process > blast_for_orthomcl (16)
[34/6a036e] Submitted process > blast_for_orthomcl (17)
[c9/eba319] Submitted process > blast_for_orthomcl (18)
[f1/b903dd] Submitted process > blast_for_orthomcl (19)
[85/30451f] Submitted process > blast_for_orthomcl (20)
[80/9bf76f] Submitted process > run_pfam (33)
[29/2c1e36] Submitted process > run_pfam (34)
[9d/3466f8] Submitted process > run_pfam (35)
[cb/c15a94] Submitted process > run_pfam (36)
[53/b7efdd] Submitted process > run_pfam (37)
[ec/8810c9] Submitted process > blast_for_orthomcl (21)
[00/9d123f] Submitted process > blast_for_orthomcl (22)
[b9/015366] Submitted process > blast_for_orthomcl (23)
[7e/012530] Submitted process > blast_for_orthomcl (24)
[27/480c4f] Submitted process > blast_for_orthomcl (25)
[10/6a11bc] Submitted process > run_pfam (38)
[0f/abd416] Submitted process > run_pfam (39)
[80/a3b3df] Submitted process > run_pfam (40)
[67/66d594] Submitted process > run_pfam (41)
[b5/1cbe38] Submitted process > run_pfam (42)
[9b/02340e] Submitted process > blast_for_orthomcl (26)
[c9/52b8af] Submitted process > blast_for_orthomcl (27)
[4a/0d8f44] Submitted process > blast_for_orthomcl (28)
[26/e00b81] Submitted process > blast_for_orthomcl (29)
[12/ae931b] Submitted process > blast_for_orthomcl (30)
[7b/cff4fe] Submitted process > run_pfam (43)
[57/a09363] Submitted process > run_pfam (44)
[2b/a96169] Submitted process > run_pfam (45)
[5e/99235a] Submitted process > run_pfam (46)
[34/be4875] Submitted process > run_pfam (47)
[6d/42a2ea] Submitted process > blast_for_orthomcl (31)
[e7/522ad9] Submitted process > blast_for_orthomcl (32)
[ad/e82546] Submitted process > blast_for_orthomcl (33)
[c9/2827a8] Submitted process > blast_for_orthomcl (34)
[12/f8b9ff] Submitted process > blast_for_orthomcl (35)
[6c/846839] Submitted process > run_pfam (48)
[15/9dc11e] Submitted process > run_pfam (49)
[84/a53684] Submitted process > run_pfam (50)
[45/6a7ba8] Submitted process > run_pfam (51)
[10/8c51df] Submitted process > run_pfam (52)
[bd/fde1f8] Submitted process > blast_for_orthomcl (36)
[94/e52f15] Submitted process > blast_for_orthomcl (37)
[bb/33e622] Submitted process > blast_for_orthomcl (38)
[c6/764d4f] Submitted process > blast_for_orthomcl (39)
[ac/d47069] Submitted process > blast_for_orthomcl (40)
[50/36d8ae] Submitted process > run_pfam (53)
[38/323e3d] Submitted process > run_pfam (54)
[78/155d94] Submitted process > run_pfam (55)
[16/03e531] Submitted process > run_pfam (56)
[ab/3d0c29] Submitted process > run_pfam (57)
[ec/0b3824] Submitted process > blast_for_orthomcl (41)
[86/ce0ade] Submitted process > blast_for_orthomcl (42)
[a2/023fe4] Submitted process > blast_for_orthomcl (43)
[05/f86bee] Submitted process > blast_for_orthomcl (44)
[47/cf82b4] Submitted process > blast_for_orthomcl (45)
[78/1388d9] Submitted process > run_pfam (58)
[5a/2bd3bf] Submitted process > run_pfam (59)
[96/a93cf8] Submitted process > run_pfam (60)
[51/ab39bf] Submitted process > run_pfam (61)
[fd/b21dfa] Submitted process > run_pfam (62)
[2b/73d23e] Submitted process > blast_for_orthomcl (46)
[c1/f3a6ec] Submitted process > blast_for_orthomcl (47)
[a3/849f7f] Submitted process > blast_for_orthomcl (48)
[26/5555fc] Submitted process > blast_for_orthomcl (49)
[0f/823f42] Submitted process > blast_for_orthomcl (50)
[90/74976f] Submitted process > run_pfam (63)
[0e/c96670] Submitted process > run_pfam (64)
[34/8fd10d] Submitted process > run_pfam (65)
[f2/eba45c] Submitted process > run_pfam (66)
[86/737fdc] Submitted process > run_pfam (67)
[0c/c6ff9f] Submitted process > blast_for_orthomcl (51)
[0c/f0fc3f] Submitted process > blast_for_orthomcl (52)
[c2/cafb61] Submitted process > blast_for_orthomcl (53)
[57/68027a] Submitted process > blast_for_orthomcl (54)
[ee/d82fde] Submitted process > blast_for_orthomcl (55)
[cf/bdc3f9] Submitted process > run_pfam (68)
[c3/d6fb51] Submitted process > run_pfam (69)
[71/068c7d] Submitted process > run_pfam (70)
[56/6a358f] Submitted process > run_pfam (71)
[d9/3baad4] Submitted process > run_pfam (72)
[39/a58345] Submitted process > blast_for_orthomcl (56)
[9b/1d72c8] Submitted process > blast_for_orthomcl (57)
[4c/9c87e4] Submitted process > blast_for_orthomcl (58)
[1b/f7299b] Submitted process > blast_for_orthomcl (59)
[08/d19eb9] Submitted process > blast_for_orthomcl (60)
[7f/e3c516] Submitted process > run_pfam (73)
[2e/a9d42e] Submitted process > run_pfam (74)
[1c/ec2287] Submitted process > run_pfam (75)
[5f/6e850b] Submitted process > run_pfam (76)
[7f/4e0688] Submitted process > run_pfam (77)
[b0/b516cf] Submitted process > blast_for_orthomcl (61)
[a4/5259a4] Submitted process > blast_for_orthomcl (62)
[2a/5f4e75] Submitted process > blast_for_orthomcl (63)
[e6/04d8d9] Submitted process > blast_for_orthomcl (64)
[94/f92d35] Submitted process > blast_for_orthomcl (65)
[3a/bc846f] Submitted process > run_pfam (78)
[09/2565d5] Submitted process > run_pfam (79)
[1b/7c2b24] Submitted process > run_pfam (80)
[24/5db5ed] Submitted process > run_pfam (81)
[27/6557d8] Submitted process > run_pfam (82)
[f5/3b58b5] Submitted process > blast_for_orthomcl (66)
[5f/b9da34] Submitted process > blast_for_orthomcl (67)
[47/ff5085] Submitted process > blast_for_orthomcl (68)
[13/264a76] Submitted process > blast_for_orthomcl (69)
[94/e6038d] Submitted process > blast_for_orthomcl (70)
[16/3e6bbe] Submitted process > run_pfam (83)
[e6/1b61f9] Submitted process > run_pfam (84)
[e6/ad4045] Submitted process > run_pfam (85)
[6d/0e922a] Submitted process > run_pfam (86)
[50/add7ed] Submitted process > run_pfam (87)
[a1/6b2c6a] Submitted process > blast_for_orthomcl (71)
[0d/39f8e4] Submitted process > blast_for_orthomcl (72)
[81/49dfe4] Submitted process > blast_for_orthomcl (73)
[ac/d7e9ca] Submitted process > blast_for_orthomcl (74)
[80/c1f6af] Submitted process > blast_for_orthomcl (75)
[64/5d1c82] Submitted process > run_pfam (88)
[7d/56cd4e] Submitted process > run_pfam (89)
[14/a5fade] Submitted process > run_pfam (90)
[df/894329] Submitted process > run_pfam (91)
[2b/732f2d] Submitted process > run_pfam (92)
[21/46d20d] Submitted process > blast_for_orthomcl (76)
[e2/a2c31f] Submitted process > blast_for_orthomcl (77)
[ed/788922] Submitted process > blast_for_orthomcl (78)
[db/8378c3] Submitted process > blast_for_orthomcl (79)
[51/41b058] Submitted process > blast_for_orthomcl (80)
[24/47b04d] Submitted process > run_pfam (93)
[46/a3bbd1] Submitted process > run_pfam (94)
[25/c8b338] Submitted process > run_pfam (95)
[f9/09a7b4] Submitted process > run_pfam (96)
[e6/c78b1a] Submitted process > run_pfam (97)
[99/925b06] Submitted process > blast_for_orthomcl (81)
[2e/4a760e] Submitted process > blast_for_orthomcl (82)
[c7/a41738] Submitted process > blast_for_orthomcl (83)
[f7/2aa85c] Submitted process > blast_for_orthomcl (84)
[64/b00cb1] Submitted process > blast_for_orthomcl (85)
[b2/77d497] Submitted process > run_pfam (98)
[87/ac4992] Submitted process > run_pfam (99)
[d9/104458] Submitted process > run_pfam (100)
[c2/d1ec58] Submitted process > run_pfam (101)
[f2/ae9508] Submitted process > run_pfam (102)
[a5/e3af1f] Submitted process > blast_for_orthomcl (86)
[97/910bc2] Submitted process > blast_for_orthomcl (87)
[38/1f6777] Submitted process > blast_for_orthomcl (88)
[20/7b8948] Submitted process > blast_for_orthomcl (89)
[56/27f108] Submitted process > blast_for_orthomcl (90)
[ce/750be3] Submitted process > run_pfam (103)
[ed/f305c9] Submitted process > run_pfam (104)
[b6/19559e] Submitted process > run_pfam (105)
[c2/809658] Submitted process > run_pfam (106)
[3f/f5f189] Submitted process > run_pfam (107)
[df/a4d01d] Submitted process > blast_for_orthomcl (91)
[ad/bb4696] Submitted process > blast_for_orthomcl (92)
[ba/da26fd] Submitted process > blast_for_orthomcl (93)
[84/fcf781] Submitted process > blast_for_orthomcl (94)
[2c/590f3d] Submitted process > blast_for_orthomcl (95)
[97/9704a7] Submitted process > run_pfam (108)
[8f/474777] Submitted process > run_pfam (109)
[6f/861479] Submitted process > run_pfam (110)
[52/03c806] Submitted process > run_pfam (111)
[c2/3876e1] Submitted process > run_pfam (112)
[81/76ac27] Submitted process > blast_for_orthomcl (96)
[93/5120ee] Submitted process > blast_for_orthomcl (97)
[13/652e32] Submitted process > blast_for_orthomcl (98)
[4f/4c8eb3] Submitted process > blast_for_orthomcl (99)
[47/9b8742] Submitted process > blast_for_orthomcl (100)
[b0/bb43f3] Submitted process > run_pfam (113)
[0a/279f7b] Submitted process > run_pfam (114)
[2a/ee9af3] Submitted process > run_pfam (115)
[8d/a51608] Submitted process > run_pfam (116)
[74/5ed907] Submitted process > run_pfam (117)
[3e/ddf8ed] Submitted process > blast_for_orthomcl (101)
[81/4f78a6] Submitted process > blast_for_orthomcl (102)
[a5/951c5d] Submitted process > blast_for_orthomcl (103)
[e6/9ec033] Submitted process > blast_for_orthomcl (104)
[08/d4b381] Submitted process > blast_for_orthomcl (105)
[56/53357e] Submitted process > run_pfam (118)
[27/926b88] Submitted process > run_pfam (119)
[c1/1c86b8] Submitted process > run_pfam (120)
[7e/2e5ff9] Submitted process > run_pfam (121)
[1e/dc47ea] Submitted process > run_pfam (122)
[f7/f9d4c5] Submitted process > blast_for_orthomcl (106)
[5b/74a906] Submitted process > blast_for_orthomcl (107)
[13/be2d8f] Submitted process > blast_for_orthomcl (108)
[1b/1d2cca] Submitted process > blast_for_orthomcl (109)
[ae/eab026] Submitted process > blast_for_orthomcl (110)
[ac/5d44e9] Submitted process > run_pfam (123)
[3e/96b6f3] Submitted process > run_pfam (124)
[39/69bfb1] Submitted process > run_pfam (125)
[d6/eb097c] Submitted process > run_pfam (126)
[d4/3b23ca] Submitted process > run_pfam (127)
[1e/10a523] Submitted process > blast_for_orthomcl (111)
[5d/c463ff] Submitted process > blast_for_orthomcl (112)
[ec/ba3286] Submitted process > blast_for_orthomcl (113)
[d3/c597ce] Submitted process > blast_for_orthomcl (114)
[fd/b0f6a0] Submitted process > blast_for_orthomcl (115)
[52/303195] Submitted process > run_pfam (128)
[dd/b7e7d7] Submitted process > run_pfam (129)
[6f/e7eefe] Submitted process > run_pfam (130)
[c5/594328] Submitted process > run_pfam (131)
[ac/673ce2] Submitted process > run_pfam (132)
[60/9dfba9] Submitted process > blast_for_orthomcl (116)
[ac/fb8b17] Submitted process > blast_for_orthomcl (117)
[29/2ccf49] Submitted process > blast_for_orthomcl (118)
[75/bd7853] Submitted process > blast_for_orthomcl (119)
[3b/2a32e4] Submitted process > blast_for_orthomcl (120)
[e3/aeb851] Submitted process > run_pfam (133)
[7e/7cb091] Submitted process > run_pfam (134)
[55/5efbf4] Submitted process > run_pfam (135)
[00/0c955e] Submitted process > run_pfam (136)
[f0/15c5d5] Submitted process > run_pfam (137)
[76/a59253] Submitted process > blast_for_orthomcl (121)
[1d/22026a] Submitted process > blast_for_orthomcl (122)
[1d/ec67fd] Submitted process > blast_for_orthomcl (123)
[fe/7fc925] Submitted process > blast_for_orthomcl (124)
[9c/24d135] Submitted process > blast_for_orthomcl (125)
[a9/e3027e] Submitted process > run_pfam (138)
[82/f30507] Submitted process > run_pfam (139)
[55/54e292] Submitted process > run_pfam (140)
[b9/126bc7] Submitted process > run_pfam (141)
[bd/3d038c] Submitted process > run_pfam (142)
[61/ec1a4d] Submitted process > blast_for_orthomcl (126)
[00/91d5da] Submitted process > blast_for_orthomcl (127)
[60/45538b] Submitted process > blast_for_orthomcl (128)
[e1/da1d61] Submitted process > blast_for_orthomcl (129)
[1b/21b214] Submitted process > blast_for_orthomcl (130)
[e9/67b957] Submitted process > run_pfam (143)
[cf/0d5bdc] Submitted process > run_pfam (144)
[df/2bf262] Submitted process > run_pfam (145)
[2f/e403b2] Submitted process > run_pfam (146)
[cd/9ce600] Submitted process > run_pfam (147)
[cd/077995] Submitted process > blast_for_orthomcl (131)
[17/7506f9] Submitted process > blast_for_orthomcl (132)
[f3/8a13b1] Submitted process > blast_for_orthomcl (133)
[5d/bf162a] Submitted process > blast_for_orthomcl (134)
[77/ce814e] Submitted process > blast_for_orthomcl (135)
[98/22c400] Submitted process > run_pfam (148)
[06/56a79b] Submitted process > run_pfam (149)
[c1/742b06] Submitted process > run_pfam (150)
[bd/2583dd] Submitted process > run_pfam (151)
[87/e5d67a] Submitted process > run_pfam (152)
[c9/14b99a] Submitted process > blast_for_orthomcl (136)
[02/260b39] Submitted process > blast_for_orthomcl (137)
[b8/13a8ce] Submitted process > blast_for_orthomcl (138)
[98/47799a] Submitted process > blast_for_orthomcl (139)
[2c/ea14b5] Submitted process > blast_for_orthomcl (140)
[63/eaa3e9] Submitted process > run_pfam (153)
[c0/1f3e17] Submitted process > run_pfam (154)
[5f/9d49a7] Submitted process > run_pfam (155)
[c2/e022d5] Submitted process > run_pfam (156)
[43/a4ff1a] Submitted process > run_pfam (157)
[c6/50354a] Submitted process > blast_for_orthomcl (141)
[ff/128f68] Submitted process > blast_for_orthomcl (142)
[df/d99fd0] Submitted process > blast_for_orthomcl (143)
[71/8ece91] Submitted process > blast_for_orthomcl (144)
[9b/9c753c] Submitted process > blast_for_orthomcl (145)
[9a/08593f] Submitted process > run_pfam (158)
[67/a80f2b] Submitted process > run_pfam (159)
[28/d88ac2] Submitted process > run_pfam (160)
[d6/31f71e] Submitted process > run_pfam (161)
[a7/9dfceb] Submitted process > run_pfam (162)
[00/a9ba49] Submitted process > blast_for_orthomcl (146)
[51/06cb66] Submitted process > blast_for_orthomcl (147)
[de/7ecc97] Submitted process > blast_for_orthomcl (148)
[f1/c2341a] Submitted process > blast_for_orthomcl (149)
[61/c4b034] Submitted process > blast_for_orthomcl (150)
[57/3a90fe] Submitted process > run_pfam (163)
[31/46789a] Submitted process > run_pfam (164)
[1e/8db380] Submitted process > run_pfam (165)
[13/23bf6a] Submitted process > run_pfam (166)
[46/30f742] Submitted process > run_pfam (167)
[d1/9177aa] Submitted process > blast_for_orthomcl (151)
[7c/ae1de7] Submitted process > blast_for_orthomcl (152)
[81/daae0c] Submitted process > blast_for_orthomcl (153)
[70/c56a43] Submitted process > blast_for_orthomcl (154)
[ce/cf95f3] Submitted process > blast_for_orthomcl (155)
[0f/a21c62] Submitted process > run_pfam (168)
[d4/5ae9d2] Submitted process > run_pfam (169)
[c8/2fbff8] Submitted process > run_pfam (170)
[a9/3135d0] Submitted process > run_pfam (171)
[5c/317218] Submitted process > run_pfam (172)
[c8/7f60bd] Submitted process > blast_for_orthomcl (156)
[a5/e06f1d] Submitted process > blast_for_orthomcl (157)
[be/3b8e80] Submitted process > blast_for_orthomcl (158)
[56/479289] Submitted process > blast_for_orthomcl (159)
[ae/1aaa9f] Submitted process > blast_for_orthomcl (160)
[c2/3c6616] Submitted process > run_pfam (173)
[d9/aba362] Submitted process > run_pfam (174)
[ea/330fa7] Submitted process > run_pfam (175)
[03/d6a4d0] Submitted process > run_pfam (176)
[c9/0fde18] Submitted process > run_pfam (177)
[c8/1a82bb] Submitted process > blast_for_orthomcl (161)
[03/c0df67] Submitted process > blast_for_orthomcl (162)
[46/5aae64] Submitted process > blast_for_orthomcl (163)
[94/156eff] Submitted process > blast_for_orthomcl (164)
[23/fbd904] Submitted process > blast_for_orthomcl (165)
[e0/63cee0] Submitted process > run_pfam (178)
[09/68dcbd] Submitted process > run_pfam (179)
[d6/e752bc] Submitted process > run_pfam (180)
[3f/bbce71] Submitted process > run_pfam (181)
[2e/e183b7] Submitted process > run_pfam (182)
[9e/079cb0] Submitted process > blast_for_orthomcl (166)
[e2/cca161] Submitted process > blast_for_orthomcl (167)
[e5/c9652a] Submitted process > blast_for_orthomcl (168)
[79/47df7a] Submitted process > blast_for_orthomcl (169)
[5e/324107] Submitted process > blast_for_orthomcl (170)
[9b/2b5631] Submitted process > run_pfam (183)
[3e/d10fb6] Submitted process > run_pfam (184)
[15/4cb7ee] Submitted process > run_pfam (185)
[d2/818d13] Submitted process > run_pfam (186)
[3c/01b9ae] Submitted process > run_pfam (187)
[ff/11a9d8] Submitted process > blast_for_orthomcl (171)
[19/0407d0] Submitted process > blast_for_orthomcl (172)
[06/343ed4] Submitted process > blast_for_orthomcl (173)
[0e/4ae38b] Submitted process > blast_for_orthomcl (174)
[58/91b8a5] Submitted process > blast_for_orthomcl (175)
[25/c92946] Submitted process > run_pfam (188)
[76/21dece] Submitted process > run_pfam (189)
[db/4f1ec9] Submitted process > run_pfam (190)
[78/a45bfa] Submitted process > run_pfam (191)
[47/b8639d] Submitted process > run_pfam (192)
[7b/4bbdf1] Submitted process > blast_for_orthomcl (176)
[20/1527bb] Submitted process > blast_for_orthomcl (177)
[4a/bc0aa2] Submitted process > blast_for_orthomcl (178)
[47/6af908] Submitted process > blast_for_orthomcl (179)
[59/d10a4f] Submitted process > blast_for_orthomcl (180)
[11/6ba45e] Submitted process > run_pfam (193)
[32/b86ed6] Submitted process > run_pfam (194)
[de/cdb37d] Submitted process > run_pfam (195)
[06/d09c40] Submitted process > run_pfam (196)
[9c/fc6c95] Submitted process > run_pfam (197)
[91/443ec0] Submitted process > blast_for_orthomcl (181)
[59/10d471] Submitted process > blast_for_orthomcl (182)
[6b/7b92ae] Submitted process > blast_for_orthomcl (183)
[6e/c274f6] Submitted process > blast_for_orthomcl (184)
[57/d4ec5f] Submitted process > blast_for_orthomcl (185)
[46/9f7231] Submitted process > run_pfam (198)
[90/70dd72] Submitted process > run_pfam (199)
[32/505deb] Submitted process > run_pfam (200)
[7a/a7cce6] Submitted process > run_pfam (201)
[b0/3cdba6] Submitted process > run_pfam (202)
[83/9afda1] Submitted process > blast_for_orthomcl (186)
[a1/d7944d] Submitted process > blast_for_orthomcl (187)
[c6/15c9e1] Submitted process > blast_for_orthomcl (188)
[05/b4d4e7] Submitted process > blast_for_orthomcl (189)
[b2/8d81f8] Submitted process > blast_for_orthomcl (190)
[7f/e3bac0] Submitted process > run_pfam (203)
[e1/8853f1] Submitted process > run_pfam (204)
[61/d92800] Submitted process > run_pfam (205)
[8a/52dba0] Submitted process > run_pfam (206)
[41/9bb55a] Submitted process > run_pfam (207)
[6e/8524f4] Submitted process > blast_for_orthomcl (191)
[0a/cf8215] Submitted process > blast_for_orthomcl (192)
[7e/ecf0d1] Submitted process > blast_for_orthomcl (193)
[24/648987] Submitted process > blast_for_orthomcl (194)
[29/4df72b] Submitted process > blast_for_orthomcl (195)
[47/ab3801] Submitted process > run_pfam (208)
[9f/fc930b] Submitted process > run_pfam (209)
[24/8feee9] Submitted process > run_pfam (210)
[2a/9ae8af] Submitted process > run_pfam (211)
[4e/418d84] Submitted process > run_pfam (212)
[68/8defc9] Submitted process > blast_for_orthomcl (196)
[3e/e5a6e2] Submitted process > blast_for_orthomcl (197)
[42/195fd0] Submitted process > blast_for_orthomcl (198)
[7c/e45890] Submitted process > blast_for_orthomcl (199)
[85/5137cb] Submitted process > blast_for_orthomcl (200)
[76/232702] Submitted process > run_pfam (213)
[6a/93ad50] Submitted process > run_pfam (214)
[78/2c5153] Submitted process > run_pfam (215)
[b8/bd74c1] Submitted process > run_pfam (216)
[60/60c95f] Submitted process > run_pfam (217)
[af/082e2b] Submitted process > blast_for_orthomcl (201)
[de/8391c2] Submitted process > blast_for_orthomcl (202)
[d8/a4e533] Submitted process > blast_for_orthomcl (203)
[44/8fc20d] Submitted process > blast_for_orthomcl (204)
[14/15b1aa] Submitted process > blast_for_orthomcl (205)
[55/3430ec] Submitted process > run_pfam (218)
[d2/a437b6] Submitted process > run_pfam (219)
[f3/660412] Submitted process > run_pfam (220)
[2a/2332dc] Submitted process > run_pfam (221)
[ee/c92e33] Submitted process > run_pfam (222)
[93/ae1711] Submitted process > blast_for_orthomcl (206)
[71/401dd4] Submitted process > blast_for_orthomcl (207)
[fb/623eec] Submitted process > blast_for_orthomcl (208)
[23/3c25f1] Submitted process > blast_for_orthomcl (209)
[a0/2a49d4] Submitted process > blast_for_orthomcl (210)
[b2/703efc] Submitted process > run_pfam (223)
[ec/cc2007] Submitted process > run_pfam (224)
[17/a11e51] Submitted process > run_pfam (225)
[37/514742] Submitted process > run_pfam (226)
[53/aa7c6c] Submitted process > run_pfam (227)
[a4/e913b9] Submitted process > blast_for_orthomcl (211)
[01/032941] Submitted process > blast_for_orthomcl (212)
[b2/94de18] Submitted process > blast_for_orthomcl (213)
[e3/9d79e6] Submitted process > blast_for_orthomcl (214)
[44/7330d9] Submitted process > blast_for_orthomcl (215)
[4e/c66396] Submitted process > run_pfam (228)
[ca/0f8ec4] Submitted process > run_pfam (229)
[5d/31f371] Submitted process > run_pfam (230)
[4d/c42801] Submitted process > run_pfam (231)
[fc/5446ad] Submitted process > run_pfam (232)
[26/8c090f] Submitted process > blast_for_orthomcl (216)
[f3/283759] Submitted process > blast_for_orthomcl (217)
[b4/5f6b4d] Submitted process > blast_for_orthomcl (218)
[3d/bb5fa6] Submitted process > blast_for_orthomcl (219)
[bd/084574] Submitted process > blast_for_orthomcl (220)
[c0/dbfead] Submitted process > run_pfam (233)
[82/ef1f58] Submitted process > run_pfam (234)
[fb/667290] Submitted process > run_pfam (235)
[30/cc518c] Submitted process > run_pfam (236)
[9f/aaeef3] Submitted process > run_pfam (237)
[80/23fc35] Submitted process > blast_for_orthomcl (221)
[fc/8843c0] Submitted process > blast_for_orthomcl (222)
[70/aef16d] Submitted process > blast_for_orthomcl (223)
[a3/698e6e] Submitted process > blast_for_orthomcl (224)
[ec/e492ae] Submitted process > blast_for_orthomcl (225)
[a0/5f8feb] Submitted process > run_pfam (238)
[d7/98aade] Submitted process > run_pfam (239)
[a4/adfc7e] Submitted process > run_pfam (240)
[b4/6d7408] Submitted process > run_pfam (241)
[d9/e8bebc] Submitted process > run_pfam (242)
[40/a9659e] Submitted process > blast_for_orthomcl (226)
[70/4b7c13] Submitted process > blast_for_orthomcl (227)
[4c/9d8e86] Submitted process > blast_for_orthomcl (228)
[11/da6272] Submitted process > blast_for_orthomcl (229)
[f9/38df91] Submitted process > blast_for_orthomcl (230)
[85/8cdfbb] Submitted process > run_pfam (243)
[91/c1c981] Submitted process > run_pfam (244)
[d2/86d06b] Submitted process > run_pfam (245)
[93/5efc35] Submitted process > run_pfam (246)
[0b/351948] Submitted process > run_pfam (247)
[d1/e44dc0] Submitted process > blast_for_orthomcl (231)
[d1/a34403] Submitted process > blast_for_orthomcl (232)
[89/4b489a] Submitted process > blast_for_orthomcl (233)
[1b/fa676f] Submitted process > blast_for_orthomcl (234)
[b8/efc725] Submitted process > blast_for_orthomcl (235)
[ad/21182c] Submitted process > run_pfam (248)
[8d/a58e1c] Submitted process > run_pfam (249)
[52/f59ed5] Submitted process > run_pfam (250)
[ce/c545ea] Submitted process > run_pfam (251)
[2a/dc9739] Submitted process > run_pfam (252)
[36/d8130f] Submitted process > blast_for_orthomcl (236)
[d7/6e5c61] Submitted process > blast_for_orthomcl (237)
[4f/a94102] Submitted process > blast_for_orthomcl (238)
[3d/2d8a3e] Submitted process > blast_for_orthomcl (239)
[9d/3c6b8d] Submitted process > blast_for_orthomcl (240)
[51/4b243c] Submitted process > run_pfam (253)
[1a/db6528] Submitted process > run_pfam (254)
[e4/2cb66e] Submitted process > run_pfam (255)
[12/d83485] Submitted process > run_pfam (256)
[d9/b01b93] Submitted process > run_pfam (257)
[38/5c8182] Submitted process > blast_for_orthomcl (241)
[82/b00a19] Submitted process > blast_for_orthomcl (242)
[57/504dd4] Submitted process > blast_for_orthomcl (243)
[d0/105934] Submitted process > blast_for_orthomcl (244)
[0a/116539] Submitted process > blast_for_orthomcl (245)
[8d/100fd8] Submitted process > run_pfam (258)
[94/b781f4] Submitted process > run_pfam (259)
[01/2a0822] Submitted process > run_pfam (260)
[0c/9ba0b9] Submitted process > run_pfam (261)
[90/f6418c] Submitted process > run_pfam (262)
[29/ed8538] Submitted process > blast_for_orthomcl (246)
[c3/b9c8a2] Submitted process > blast_for_orthomcl (247)
[f8/b9e752] Submitted process > blast_for_orthomcl (248)
[61/524d71] Submitted process > blast_for_orthomcl (249)
[36/f0675e] Submitted process > blast_for_orthomcl (250)
[d9/47bdb3] Submitted process > run_pfam (263)
[c5/8326ec] Submitted process > run_pfam (264)
[e7/12e904] Submitted process > run_pfam (265)
[57/5698ae] Submitted process > run_pfam (266)
[a4/408850] Submitted process > run_pfam (267)
[c2/8b0b7e] Submitted process > blast_for_orthomcl (251)
[a3/9875d4] Submitted process > blast_for_orthomcl (252)
[14/c76028] Submitted process > blast_for_orthomcl (253)
[b5/1f33fc] Submitted process > blast_for_orthomcl (254)
[d8/c39d18] Submitted process > blast_for_orthomcl (255)
[78/059346] Submitted process > run_pfam (268)
[30/056b87] Submitted process > run_pfam (269)
[99/dae77f] Submitted process > run_pfam (270)
[8f/18ee83] Submitted process > run_pfam (271)
[c8/8207e2] Submitted process > run_pfam (272)
[9f/d1258d] Submitted process > blast_for_orthomcl (256)
[d5/632013] Submitted process > blast_for_orthomcl (257)
[bb/4ec96a] Submitted process > blast_for_orthomcl (258)
[c4/0d0689] Submitted process > blast_for_orthomcl (259)
[63/05c617] Submitted process > blast_for_orthomcl (260)
[72/f0eea8] Submitted process > run_pfam (273)
[f9/dd33cd] Submitted process > run_pfam (274)
[38/d2142d] Submitted process > run_pfam (275)
[32/88b603] Submitted process > run_pfam (276)
[01/dca668] Submitted process > run_pfam (277)
[c7/0f9add] Submitted process > blast_for_orthomcl (261)
[87/f62dd2] Submitted process > blast_for_orthomcl (262)
[9f/b80d88] Submitted process > blast_for_orthomcl (263)
[06/13c65c] Submitted process > blast_for_orthomcl (264)
[59/67de47] Submitted process > blast_for_orthomcl (265)
[fd/7fda0d] Submitted process > run_pfam (278)
[4a/5ea581] Submitted process > run_pfam (279)
[72/d76c60] Submitted process > run_pfam (280)
[9c/a5a160] Submitted process > run_pfam (281)
[e1/c2424f] Submitted process > run_pfam (282)
[16/5bed9a] Submitted process > blast_for_orthomcl (266)
[43/1c0069] Submitted process > blast_for_orthomcl (267)
[da/b1f0e7] Submitted process > blast_for_orthomcl (268)
[3e/b5c11d] Submitted process > blast_for_orthomcl (269)
[42/bba497] Submitted process > blast_for_orthomcl (270)
[34/c79375] Submitted process > run_pfam (283)
[e6/025ee4] Submitted process > run_pfam (284)
[4d/a7b89c] Submitted process > run_pfam (285)
[d2/4fb917] Submitted process > run_pfam (286)
[40/9e5b4b] Submitted process > run_pfam (287)
[c4/d17bde] Submitted process > blast_for_orthomcl (271)
[3b/46e1ee] Submitted process > blast_for_orthomcl (272)
[ec/bd8791] Submitted process > blast_for_orthomcl (273)
[29/63ba14] Submitted process > blast_for_orthomcl (274)
[b2/cbd7ed] Submitted process > blast_for_orthomcl (275)
[63/7c849c] Submitted process > run_pfam (288)
[64/ba6c86] Submitted process > run_pfam (289)
[57/e70989] Submitted process > run_pfam (290)
[6c/1fad5f] Submitted process > run_pfam (291)
[4e/dfad38] Submitted process > run_pfam (292)
[6d/eb23ec] Submitted process > blast_for_orthomcl (276)
[d3/535392] Submitted process > blast_for_orthomcl (277)
[4d/83ef56] Submitted process > blast_for_orthomcl (278)
[78/1410cf] Submitted process > blast_for_orthomcl (279)
[ff/c4a8b9] Submitted process > blast_for_orthomcl (280)
[85/99d82a] Submitted process > run_pfam (293)
[d5/26de12] Submitted process > blast_for_orthomcl (281)
[c5/42d04b] Submitted process > blast_for_orthomcl (282)
[78/a79f8d] Submitted process > blast_for_orthomcl (283)
[6a/3b244f] Submitted process > blast_for_orthomcl (284)
[c2/09c34b] Submitted process > blast_for_orthomcl (285)
[8d/efd071] Submitted process > blast_for_orthomcl (286)
[c5/5a0129] Submitted process > pfam_to_gff3 (1)
[db/fe99b0] Submitted process > blast_for_orthomcl (287)
[13/fd312d] Submitted process > blast_for_orthomcl (288)
[00/ad60fc] Submitted process > blast_for_orthomcl (289)
[a5/53212a] Submitted process > blast_for_orthomcl (290)
[1a/b15d84] Submitted process > blast_for_orthomcl (291)
[c5/c624ba] Submitted process > blast_for_orthomcl (292)
[f1/4c2603] Submitted process > blast_for_orthomcl (293)
[22/997c66] Submitted process > blast_for_orthomcl (294)
[dc/dca226] Submitted process > blast_for_orthomcl (295)
[74/569457] Submitted process > blast_for_orthomcl (296)
[f5/3b13e2] Submitted process > blast_for_orthomcl (297)
[8c/8b1e7e] Submitted process > blast_for_orthomcl (298)
[4b/4013c2] Submitted process > blast_for_orthomcl (299)
[7b/5e81f0] Submitted process > blast_for_orthomcl (300)
[c9/d5960e] Submitted process > blast_for_orthomcl (301)
[18/91097a] Submitted process > blast_for_orthomcl (302)
[3b/5051c8] Submitted process > blast_for_orthomcl (303)
[1e/16b8bc] Submitted process > blast_for_orthomcl (304)
[4d/7f7289] Submitted process > blast_for_orthomcl (305)
[87/f612e5] Submitted process > blast_for_orthomcl (306)
[2b/8edd12] Submitted process > blast_for_orthomcl (307)
[7d/93dd96] Submitted process > blast_for_orthomcl (308)
[f5/182555] Submitted process > blast_for_orthomcl (309)
[1e/2664be] Submitted process > blast_for_orthomcl (310)
[8b/64afae] Submitted process > blast_for_orthomcl (311)
[bc/fcbe83] Submitted process > blast_for_orthomcl (312)
[11/9201a3] Submitted process > blast_for_orthomcl (313)
[2c/c03678] Submitted process > blast_for_orthomcl (314)
[a4/801521] Submitted process > blast_for_orthomcl (315)
[1c/95d576] Submitted process > blast_for_orthomcl (316)
[4c/b92a9b] Submitted process > blast_for_orthomcl (317)
[01/edb7e9] Submitted process > blast_for_orthomcl (318)
[f3/bf439c] Submitted process > blast_for_orthomcl (319)
[89/4d44e2] Submitted process > blast_for_orthomcl (320)
[5d/02d9df] Submitted process > blast_for_orthomcl (321)
[24/cff44d] Submitted process > blast_for_orthomcl (322)
[d3/0297f3] Submitted process > blast_for_orthomcl (323)
[0f/302562] Submitted process > blast_for_orthomcl (324)
[40/5cc20e] Submitted process > blast_for_orthomcl (325)
[f7/c6255f] Submitted process > blast_for_orthomcl (326)
[28/c0372b] Submitted process > blast_for_orthomcl (327)
[13/8f81ec] Submitted process > blast_for_orthomcl (328)
[11/51f612] Submitted process > blast_for_orthomcl (329)
[d5/fa1f25] Submitted process > blast_for_orthomcl (330)
[fd/4fcade] Submitted process > blast_for_orthomcl (331)
[90/c4b7b6] Submitted process > blast_for_orthomcl (332)
[d9/c3d32b] Submitted process > blast_for_orthomcl (333)
[9a/427f20] Submitted process > blast_for_orthomcl (334)
[be/8a8a18] Submitted process > blast_for_orthomcl (335)
[42/4e8938] Submitted process > blast_for_orthomcl (336)
[e3/e62188] Submitted process > blast_for_orthomcl (337)
[31/34f003] Submitted process > blast_for_orthomcl (338)
[18/621ada] Submitted process > blast_for_orthomcl (339)
[3c/39883f] Submitted process > blast_for_orthomcl (340)
[e6/b8ab6f] Submitted process > blast_for_orthomcl (341)
[b3/c8ac97] Submitted process > blast_for_orthomcl (342)
[9f/2932ea] Submitted process > run_orthomcl (1)
[92/0147a5] Submitted process > annotate_orthologs (1)
[b2/aec4a9] Submitted process > annotate_pfam (1)
[90/f1a0b7] Submitted process > make_distribution_gaf (1)
[60/6aa206] Submitted process > make_distribution_gff (1)
[df/c029b6] Submitted process > add_products_to_protein_fasta (1)
[1f/8fd2a0] Submitted process > make_genelist (1)
[b2/4698a2] Submitted process > merge_gff3_for_gff3toembl (1)
[ec/7a8356] Submitted process > make_genome_stats (1)
[79/af8576] Submitted process > make_report (1)
[02/fddee7] Submitted process > reference_compare (1)
[29/c961f4] Submitted process > make_circos_inputs (1)
[a5/4b1ea6] Submitted process > make_embl (1)
[84/5377ac] Submitted process > make_tree (1)
[55/9575d9] Submitted process > circos_run_chrs (29)
[4f/b2f8c8] Submitted process > circos_run_chrs (35)
[c7/84f071] Submitted process > circos_run_chrs (09)
[1c/bdd260] Submitted process > circos_run_bin (1)
[c4/47b7a0] Submitted process > circos_run_chrs (07)
[03/e59117] Submitted process > circos_run_chrs (19)
[0b/636b1e] Submitted process > circos_run_chrs (15)
[8a/f21463] Submitted process > circos_run_chrs (27)
[e6/6d036a] Submitted process > circos_run_chrs (17)
[ed/a60045] Submitted process > circos_run_chrs (13)
[2f/9b9582] Submitted process > circos_run_chrs (21)
[51/9f41b0] Submitted process > circos_run_chrs (33)
[94/3b71da] Submitted process > circos_run_chrs (23)
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The parameters you have chosen for your L_aet.scaf.trunc.fasta vs. Leishmania major Friedlin run are:
Pseudochromosomes
Protein evidence
RATT
RATT transfer type Species
SNAP
Max gene length 80000
Score threshold 0.8
Transcript evidence

Information available in the result tabs

Genome statistics

The Genome statistics tab summarizes basic numeric statistics about the annotated genome, such as

  • gene counts
  • gene density
  • GC content

This summary is useful to quickly assess the success of the annotation job: does the amount of annotated features match the expectations?

Ss stats c3ebdd445744fc3ca1698a9859e7ca56a848a84fcdba5fbfc5be90fa47f37c5c

Ss results ebaabc0d00c43a73e84c088026ac47775422a831ac4f695bb92eaae5c1bee9c9

Result files

The next tab (Result files) allows the user to download the results of the annotation jobs to their own computer, e.g. for further downstream analyses, manual curation or preparation for database submission. These are offered in the following formats:

  • GFF3 and EMBL format for annotated features
  • FASTA format for sequences
  • GAF format for GO terms for each functionally annotated gene
  • AGP format files for pseudochromosome layouts

If no pseudochromosome contiguation was selected, files for both levels are identical. We also calculate MD5 tags which may be required at the time of submission in case there is no need for further curation.


Orthology

The Venn diagram on the Orthology tab depicts shared gene cluster membership between the newly annotated genome and the reference to easily assess the amount of species-specific gene content. The set on the left (green) represents the target genome while the one on the right (blue) represents the reference. The numbers in the set circles specify the number of shared or species-specific clusters with at least two genes. The amount of genes not appearing in any cluster (singletons) is shown outside both sets.

By clicking on the numbers in the diagram, it is possible to browse the content of all sets using interactive tables. These paginated and searchable tables are shown below the Venn diagram when a number is clicked. A flat text file (in OrthoMCL 1.4 format) is also provided for custom analyses.

Ss venn 20e8e34d7910914b2e2e8eba3b19fed16d3cf3db5389ea246bb726da5be8fd20

Ss tree ed8154d9b278d860e008e64b60791b09e4196ffa78ae790bb74c71a6cd26b872

Phylogeny

The tree on the Phylogeny tab shows how the newly annotated target genome fits into the phylogeny of related species. From a set of up to 50 single-copy genes shared among all these species, a quick tree is built and visualized in an interactive tree, supporting various tree styles. All data used to build the tree are also available for download.


Synteny

The Synteny tab contains circular plots showing alignments between each reference chromosome and their newly annotated counterpart. The reference chromosome is shown at the top and the new pseudochromosome is shown at the bottom. Grey ribbons between both represent similar regions as identified by BLASTN matches. Genes on the forward strand (blue) and the reverse strand (red) are annotated on the chromosomes, as well as gaps (yellow), singletons (black) and missing core genes (green), each in separate tracks. A similar output is created for uncontiguated input sequences concatenated into a 'bin' sequence (not drawn to scale) compared to all reference chromosomes.

These plots are useful to visualize the reference-target colinearity, which helps in identifying potential problems in pseudochromosome contiguation or large-scale chromosomal rearrangements at a glance.

Ss circos 876c9094a84bacf78315a1e6ad7d304c443f0d8cb250f72b5fc8b0a973fce33d

Ss validator c00cbb12d5071d24a5bd0f69126cdf25bff229b5658018c1ceb3ac27029d2eea

Validator results

We are doing our best to ensure that gene annotation files delivered by Companion are both syntactically and semantically (=biologically) valid and do not contain major issues. However, due to the complexity of the process and the high variability of input data, it is sometimes possible to end up with less than perfect gene models. Often such remaining issues can be quickly addressed by a human curator.

To make the best use of curator time as a scarce resource, we perform thorough automatic checking of our generated annotations, given as annotation graphs in GFF3 format. The results of this check are presented in a table, grouped by feature type. The number of successful and failed checks is concisely presented and for each failed check, the ID of the questionable feature is reported by clicking on the red labels denoting checking failures. This makes it easy to quickly estimate the amount of required curation and allows to work in a directed and focused fashion.