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 8 days ago!). Click the tabs to see what data they contain.

 
Reference Query
Number of annotated regions/sequences 9 8
Number of genes 6459 5918
Gene density (genes/megabase) 398.2
Number of coding genes 6212 5821
Number of pseudogenes 194
Number of genes with function 5674
Number of pseudogenes with function 185
Number of non-coding genes 247 97
Number of genes with multiple CDSs 443
Overall GC% 33.25
Coding GC% 34.89
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These clusters have been created using OrthoMCL v2.0 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 2.0 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: CDUB.

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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 8 images (ZIP)

  • Chr1a c albicans sc5314 1A_C_albicans_SC5314
  • Chr2a c albicans sc5314 2A_C_albicans_SC5314
  • Chr3a c albicans sc5314 3A_C_albicans_SC5314
  • Chr4a c albicans sc5314 4A_C_albicans_SC5314
  • Chr5a c albicans sc5314 5A_C_albicans_SC5314
  • Chr6a c albicans sc5314 6A_C_albicans_SC5314
  • Chr7a c albicans sc5314 7A_C_albicans_SC5314
  • Chrra c albicans sc5314 RA_C_albicans_SC5314

Standard output:

N E X T F L O W  ~  version 21.10.6
Launching `/home/companion/annot-nf/annot.nf` [elated_ekeblad] - revision: 887926d855
WARN: It appears you have never run this project before -- Option `-resume` is ignored

C O M P A N I O N  ~  version 1.0.2
query               : /www/companion/annot-web/public/system/dragonfly/production/2022/11/25/62oe7mwanu_FungiDB_60_CdubliniensisCD36_Genome.fasta
reference           : Candida_albicans_SC5314
reference directory : /data/references/ref_fungidb/Ref_Candida
output directory    : /www/companion/annot-web/public/jobs/40f49c0c48d95b4deb8e5e8b

WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition -- check channel `ncrna_cmindex`
WARN: Access to undefined parameter `TRANSCRIPT_FILE` -- Initialise it to a default value eg. `params.TRANSCRIPT_FILE = some_value`
WARN: The access of `config` object is deprecated
[a9/5c4ae9] Submitted process > truncate_input_headers
WARN: The `into` operator should be used to connect two or more target channels -- consider to replace it with `.set { integrated_gff3_processed }`
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition -- check channel `pseudochr_last_index`
[22/d28817] Submitted process > press_ncRNA_cms
[af/aafece] Submitted process > exonerate_empty_hints
[dd/47948f] Submitted process > ratt_make_ref_embl
[80/fdc902] Submitted process > transcript_empty_hints
[47/30e190] Submitted process > make_empty_snap
[53/cd539f] Submitted process > pseudogene_indexing
[c2/2be1fb] Submitted process > make_ref_input_for_orthomcl
[f3/5ef449] Submitted process > prepare_orthomcl_config
[85/7232a0] Submitted process > merge_hints
[4f/3ac3b4] Submitted process > sanitize_input
[c2/a60830] Submitted process > contiguate_pseudochromosomes
[d4/f376f7] Submitted process > predict_tRNA
[79/b7f697] Submitted process > nucmer_for_circos (9)
[2b/93b59b] Submitted process > nucmer_for_circos (6)
[c4/43f059] Submitted process > nucmer_for_circos (8)
[3b/20d37a] Submitted process > nucmer_for_circos (1)
[c5/54bf2e] Submitted process > make_distribution_seqs
[16/2dd6b4] Submitted process > nucmer_for_circos (3)
[0c/b11168] Submitted process > nucmer_for_circos (4)
[87/9fe53a] Submitted process > nucmer_for_circos (5)
[54/d0d62d] Submitted process > nucmer_for_circos (7)
[7e/5cdde2] Submitted process > nucmer_for_circos (2)
[4b/9e9e3e] Submitted process > run_braker_pseudo
[26/577c33] Submitted process > run_braker_contigs
[1e/f0c0d9] Submitted process > run_ratt
[2f/b55f89] Submitted process > pseudogene_last (1)
[99/0d2537] Submitted process > predict_ncRNA (1)
[36/e9cd98] Submitted process > pseudogene_last (2)
[49/5e9f04] Submitted process > predict_ncRNA (2)
WARN: Access to undefined parameter `print_paths` -- Initialise it to a default value eg. `params.print_paths = some_value`
[bd/a09143] Submitted process > pseudogene_last (3)
[9c/b22600] Submitted process > ratt_to_gff3
[bd/f6dff3] Submitted process > merge_ncrnas (1)
[bb/b0a9b1] Submitted process > parse_braker_pseudo
[22/faf611] Submitted process > parse_braker_contigs
[3d/b01ae6] Submitted process > merge_genemodels
[05/a8df8b] Submitted process > integrate_genemodels
[1b/5eee00] Submitted process > remove_exons
[7c/25d06b] Submitted process > pseudogene_calling (1)
[5b/5c2a64] Submitted process > merge_structural (1)
[8d/de0313] Submitted process > add_gap_features (1)
[e8/aae248] Submitted process > split_splice_models_at_gaps (1)
[3d/b3f2a6] Submitted process > add_polypeptides (1)
[fb/77748a] Submitted process > get_proteins_for_orthomcl (1)
[44/040e46] Submitted process > run_pfam (1)
[71/a84d1c] Submitted process > run_pfam (2)
[bc/f686cc] Submitted process > run_pfam (4)
[58/35468b] Submitted process > run_pfam (3)
[2f/dffd8d] Submitted process > run_pfam (5)
[9c/b5e71a] Submitted process > run_pfam (6)
[9b/d8ec2a] Submitted process > run_pfam (7)
[4a/4c4cb1] Submitted process > run_pfam (8)
[18/5175d8] Submitted process > run_pfam (9)
[b4/056c29] Submitted process > run_pfam (12)
[b3/6a4ac9] Submitted process > run_pfam (11)
[d5/4fca2a] Submitted process > run_pfam (13)
[2a/ccbacb] Submitted process > run_pfam (10)
[20/65e79c] Submitted process > run_pfam (14)
[5d/34d9e0] Submitted process > run_pfam (15)
[d4/d31417] Submitted process > run_pfam (16)
[13/f0b89b] Submitted process > make_target_input_for_orthomcl (1)
[ac/44d801] Submitted process > run_pfam (17)
[75/17796b] Submitted process > run_pfam (18)
[ad/9fca19] Submitted process > run_pfam (19)
[56/d599f9] Submitted process > run_pfam (20)
[a7/9e19ff] Submitted process > run_pfam (21)
[a6/a19ea4] Submitted process > run_pfam (22)
[6c/ac56c5] Submitted process > run_pfam (23)
[8c/7dc40e] Submitted process > run_pfam (24)
[a7/b5fec7] Submitted process > run_pfam (25)
[bc/fa22bc] Submitted process > run_pfam (26)
[37/2e4751] Submitted process > run_pfam (27)
[1b/c5fa15] Submitted process > run_pfam (28)
[93/76fa07] Submitted process > run_pfam (29)
[3e/4987c3] Submitted process > run_pfam (30)
[60/a75264] Submitted process > run_pfam (31)
[35/7eb7a1] Submitted process > run_pfam (32)
[61/efe95a] Submitted process > run_pfam (33)
[68/2c402e] Submitted process > run_pfam (34)
[d3/3062d8] Submitted process > run_pfam (35)
[a8/73739e] Submitted process > run_pfam (36)
[0a/22707d] Submitted process > run_pfam (37)
[ac/cd6922] Submitted process > run_pfam (38)
[68/544f63] Submitted process > run_pfam (39)
[27/be570f] Submitted process > run_pfam (40)
[06/55d21e] Submitted process > run_pfam (41)
[7b/6ad8a4] Submitted process > run_pfam (42)
[99/d2f8a1] Submitted process > run_pfam (43)
[ad/9179dc] Submitted process > run_pfam (44)
[e0/5b47ed] Submitted process > run_pfam (45)
[0b/f62924] Submitted process > run_pfam (46)
[a4/2760ef] Submitted process > run_pfam (47)
[48/b4e240] Submitted process > run_pfam (48)
[da/cf269e] Submitted process > run_pfam (49)
[60/e87101] Submitted process > run_pfam (50)
[e6/1bfa1a] Submitted process > run_pfam (51)
[a0/bc4b32] Submitted process > run_pfam (52)
[af/514e67] Submitted process > run_pfam (53)
[36/dc2e35] Submitted process > run_pfam (54)
[18/d34b3c] Submitted process > run_pfam (55)
[23/85e9b0] Submitted process > run_pfam (56)
[e3/e1a865] Submitted process > run_pfam (57)
[fa/73e630] Submitted process > run_pfam (58)
[58/8e60fb] Submitted process > run_pfam (59)
[7b/674184] Submitted process > run_pfam (60)
[e1/01d089] Submitted process > run_pfam (61)
[0a/18742f] Submitted process > run_pfam (62)
[bb/e7c1eb] Submitted process > run_pfam (63)
[2d/5465d9] Submitted process > run_pfam (64)
[ad/c0197d] Submitted process > run_pfam (65)
[2f/86aa24] Submitted process > run_pfam (66)
[48/3c491b] Submitted process > run_pfam (67)
[2e/1a181f] Submitted process > run_pfam (68)
[d0/74b257] Submitted process > run_pfam (69)
[50/5aba87] Submitted process > run_pfam (70)
[54/e95b08] Submitted process > run_pfam (71)
[fe/1b88a5] Submitted process > run_pfam (72)
[c1/f3f360] Submitted process > run_pfam (73)
[8b/d7e4bd] Submitted process > run_pfam (74)
[af/c88633] Submitted process > run_pfam (75)
[f4/cc8dd9] Submitted process > run_pfam (76)
[71/12df7a] Submitted process > run_pfam (77)
[7c/653e2b] Submitted process > run_pfam (78)
[11/152af8] Submitted process > run_pfam (79)
[92/7f6379] Submitted process > run_pfam (80)
[4a/026307] Submitted process > run_pfam (81)
[e3/c35170] Submitted process > run_pfam (82)
[8d/5a0ea1] Submitted process > run_pfam (83)
[a9/6c3ac7] Submitted process > run_pfam (84)
[90/30a2bd] Submitted process > run_pfam (85)
[4d/35ee86] Submitted process > run_pfam (86)
[ce/bed899] Submitted process > run_pfam (87)
[49/09c693] Submitted process > run_pfam (88)
[59/fa785f] Submitted process > run_pfam (89)
[65/d6381e] Submitted process > run_pfam (90)
[2d/31e59c] Submitted process > run_pfam (91)
[49/ceb90b] Submitted process > run_pfam (92)
[5c/5e93a0] Submitted process > run_pfam (93)
[93/03c6f8] Submitted process > run_pfam (94)
[19/e7e139] Submitted process > run_pfam (95)
[d3/0f9500] Submitted process > run_pfam (96)
[95/d21f66] Submitted process > run_pfam (97)
[be/4b96f0] Submitted process > run_pfam (98)
[76/06ce16] Submitted process > run_pfam (99)
[ed/1ce429] Submitted process > run_pfam (100)
[23/215523] Submitted process > run_pfam (101)
[be/c6c05a] Submitted process > run_pfam (102)
[c8/0fd49c] Submitted process > run_pfam (103)
[5d/f926a1] Submitted process > run_pfam (104)
[bb/8b8b76] Submitted process > run_pfam (105)
[59/0f1a53] Submitted process > run_pfam (106)
[d0/5ddc89] Submitted process > run_pfam (107)
[7a/8aa700] Submitted process > run_pfam (108)
[47/ef2f99] Submitted process > run_pfam (109)
[3b/60644c] Submitted process > run_pfam (110)
[b7/e23428] Submitted process > run_pfam (111)
[9a/880e9a] Submitted process > run_pfam (112)
[2f/2394db] Submitted process > run_pfam (113)
[4a/596c99] Submitted process > run_pfam (114)
[b7/af37cd] Submitted process > run_pfam (115)
[09/9d2a10] Submitted process > run_pfam (116)
[fa/2cd254] Submitted process > run_pfam (117)
[e0/2f55d8] Submitted process > run_pfam (118)
[a7/3e9b8b] Submitted process > run_pfam (119)
[df/9608e5] Submitted process > run_pfam (120)
[82/68800d] Submitted process > run_pfam (121)
[b6/8499d4] Submitted process > run_pfam (122)
[cc/95625f] Submitted process > run_pfam (123)
[d4/2439f8] Submitted process > run_pfam (124)
[20/6305d0] Submitted process > run_pfam (125)
[ef/afa82a] Submitted process > run_pfam (126)
[ed/3d943b] Submitted process > run_pfam (127)
[60/392a8c] Submitted process > run_pfam (128)
[11/18530a] Submitted process > run_pfam (129)
[31/312685] Submitted process > run_pfam (130)
[61/7ffeab] Submitted process > run_pfam (131)
[a4/9af396] Submitted process > run_pfam (132)
[79/8d1465] Submitted process > run_pfam (133)
[4a/ce5f47] Submitted process > run_pfam (134)
[70/41adfe] Submitted process > run_pfam (135)
[2d/0856f6] Submitted process > run_pfam (136)
[be/b14bbd] Submitted process > run_pfam (137)
[59/829160] Submitted process > run_pfam (138)
[10/6411fb] Submitted process > run_pfam (139)
[c7/ba0f51] Submitted process > run_pfam (140)
[bc/62a7ab] Submitted process > run_pfam (141)
[7e/37a8f1] Submitted process > run_pfam (142)
[5e/d831df] Submitted process > run_pfam (143)
[bf/0a0324] Submitted process > run_pfam (144)
[90/ef27f6] Submitted process > run_pfam (145)
[67/ff7f32] Submitted process > run_pfam (146)
[60/189561] Submitted process > run_pfam (147)
[36/24a588] Submitted process > run_pfam (148)
[bc/eddaa8] Submitted process > run_pfam (149)
[1a/0fd827] Submitted process > run_pfam (150)
[47/93398f] Submitted process > run_pfam (151)
[c2/93c58d] Submitted process > run_pfam (152)
[4c/6f538e] Submitted process > run_pfam (153)
[b8/53a36b] Submitted process > run_pfam (154)
[07/319118] Submitted process > run_pfam (155)
[36/709864] Submitted process > run_pfam (156)
[7f/4b9648] Submitted process > run_pfam (157)
[7b/83f39f] Submitted process > run_pfam (158)
[66/48e7a7] Submitted process > run_pfam (159)
[73/ec5c8f] Submitted process > run_pfam (160)
[0d/0444f9] Submitted process > run_pfam (161)
[f0/358162] Submitted process > run_pfam (162)
[b9/f1a710] Submitted process > run_pfam (163)
[67/18c734] Submitted process > run_pfam (164)
[0d/d6e379] Submitted process > run_pfam (165)
[df/fb9760] Submitted process > run_pfam (166)
[1c/de5ea7] Submitted process > run_pfam (167)
[8a/ffbe2a] Submitted process > run_pfam (168)
[3d/04aad1] Submitted process > run_pfam (169)
[92/4582f5] Submitted process > run_pfam (170)
[d1/6f1a2c] Submitted process > run_pfam (171)
[f1/3e3096] Submitted process > run_pfam (172)
[63/406c69] Submitted process > run_pfam (173)
[b8/eb984c] Submitted process > run_pfam (174)
[7c/fd3b5b] Submitted process > run_pfam (175)
[e4/22fcf3] Submitted process > run_pfam (176)
[a0/51a242] Submitted process > run_pfam (177)
[80/a44ed3] Submitted process > run_pfam (178)
[df/cf969e] Submitted process > run_pfam (179)
[a3/ef8025] Submitted process > run_pfam (180)
[e8/4de7d5] Submitted process > run_pfam (181)
[f2/757c0b] Submitted process > run_pfam (182)
[ec/aa3fd5] Submitted process > run_pfam (183)
[6a/c8e187] Submitted process > run_pfam (184)
[63/af96c0] Submitted process > run_pfam (185)
[e4/66c725] Submitted process > run_pfam (186)
[fa/888d60] Submitted process > run_pfam (187)
[1e/876a33] Submitted process > run_pfam (188)
[ae/4b79e7] Submitted process > run_pfam (189)
[26/ee7690] Submitted process > run_pfam (190)
[30/5790d9] Submitted process > run_pfam (191)
[08/50f7c9] Submitted process > run_pfam (192)
[1f/04ef7e] Submitted process > run_pfam (193)
[22/dbd0d1] Submitted process > run_pfam (194)
[90/096da8] Submitted process > run_pfam (195)
[2c/ebb7e4] Submitted process > run_pfam (196)
[b3/621c20] Submitted process > run_pfam (197)
[74/ea645d] Submitted process > run_pfam (198)
[21/8bd238] Submitted process > run_pfam (199)
[85/3046b4] Submitted process > run_pfam (200)
[21/9fbcfd] Submitted process > run_pfam (201)
[3a/de0d94] Submitted process > run_pfam (202)
[fd/331e64] Submitted process > filter_fasta_for_orthomcl (1)
[63/6948ab] Submitted process > blast_for_orthomcl_formatdb (1)
[7f/d27479] Submitted process > blast_for_orthomcl (5)
[2c/257f0d] Submitted process > blast_for_orthomcl (15)
[e3/6c6238] Submitted process > blast_for_orthomcl (1)
[29/e6aeed] Submitted process > blast_for_orthomcl (13)
[f4/2f25a7] Submitted process > blast_for_orthomcl (6)
[04/e039bd] Submitted process > blast_for_orthomcl (7)
[d4/3c6682] Submitted process > blast_for_orthomcl (12)
[3a/21bdc3] Submitted process > blast_for_orthomcl (14)
[74/183b42] Submitted process > blast_for_orthomcl (4)
[f2/757285] Submitted process > blast_for_orthomcl (9)
[09/38059c] Submitted process > blast_for_orthomcl (3)
[1a/4fb304] Submitted process > blast_for_orthomcl (11)
[85/85827b] Submitted process > blast_for_orthomcl (10)
[70/07a672] Submitted process > blast_for_orthomcl (16)
[5e/71e5f2] Submitted process > blast_for_orthomcl (2)
[37/ce0bb0] Submitted process > blast_for_orthomcl (8)
[4a/d9067a] Submitted process > blast_for_orthomcl (17)
[c0/587375] Submitted process > blast_for_orthomcl (18)
[a0/314908] Submitted process > blast_for_orthomcl (19)
[80/f3c5c3] Submitted process > blast_for_orthomcl (20)
[58/9a3b08] Submitted process > blast_for_orthomcl (21)
[48/c5b333] Submitted process > blast_for_orthomcl (22)
[0d/5d7875] Submitted process > blast_for_orthomcl (23)
[9e/aaef6c] Submitted process > blast_for_orthomcl (24)
[6e/2279c6] Submitted process > blast_for_orthomcl (25)
[56/573671] Submitted process > blast_for_orthomcl (26)
[b3/793991] Submitted process > blast_for_orthomcl (27)
[56/ef45ef] Submitted process > blast_for_orthomcl (28)
[61/038cc7] Submitted process > blast_for_orthomcl (29)
[0e/d0f7a9] Submitted process > blast_for_orthomcl (30)
[80/f3899c] Submitted process > blast_for_orthomcl (31)
[30/49ce55] Submitted process > blast_for_orthomcl (32)
[af/92a6dd] Submitted process > blast_for_orthomcl (33)
[30/e6d48a] Submitted process > blast_for_orthomcl (34)
[88/4280f3] Submitted process > blast_for_orthomcl (35)
[61/8591e2] Submitted process > blast_for_orthomcl (36)
[56/588993] Submitted process > blast_for_orthomcl (37)
[45/03ce13] Submitted process > blast_for_orthomcl (38)
[ba/3a4936] Submitted process > blast_for_orthomcl (39)
[bb/2fd54a] Submitted process > blast_for_orthomcl (40)
[4c/a44e9b] Submitted process > blast_for_orthomcl (41)
[38/5b9aad] Submitted process > blast_for_orthomcl (42)
[39/816f77] Submitted process > blast_for_orthomcl (43)
[be/8a7ece] Submitted process > blast_for_orthomcl (44)
[59/19a417] Submitted process > blast_for_orthomcl (45)
[ba/3cbeb1] Submitted process > blast_for_orthomcl (46)
[96/b754c0] Submitted process > blast_for_orthomcl (47)
[f0/e03381] Submitted process > blast_for_orthomcl (48)
[0e/b5225c] Submitted process > blast_for_orthomcl (49)
[c7/12100e] Submitted process > blast_for_orthomcl (50)
[94/96c9ba] Submitted process > blast_for_orthomcl (51)
[4e/6c135e] Submitted process > blast_for_orthomcl (52)
[5e/efc814] Submitted process > blast_for_orthomcl (53)
[e7/8d5aad] Submitted process > blast_for_orthomcl (54)
[c9/00d1d5] Submitted process > blast_for_orthomcl (55)
[71/9ff3bd] Submitted process > blast_for_orthomcl (56)
[56/5bd500] Submitted process > blast_for_orthomcl (57)
[69/809df1] Submitted process > blast_for_orthomcl (59)
[78/512f95] Submitted process > blast_for_orthomcl (58)
[04/3c7b7f] Submitted process > blast_for_orthomcl (60)
[27/13e866] Submitted process > blast_for_orthomcl (61)
[7e/712588] Submitted process > blast_for_orthomcl (62)
[40/184673] Submitted process > blast_for_orthomcl (63)
[13/60bf0c] Submitted process > blast_for_orthomcl (64)
[73/e0dd9b] Submitted process > blast_for_orthomcl (65)
[b8/45464b] Submitted process > blast_for_orthomcl (66)
[6b/a8589a] Submitted process > blast_for_orthomcl (67)
[cf/e21699] Submitted process > blast_for_orthomcl (68)
[41/ea865c] Submitted process > blast_for_orthomcl (69)
[dc/871630] Submitted process > blast_for_orthomcl (70)
[15/7fec63] Submitted process > blast_for_orthomcl (71)
[76/80ce65] Submitted process > blast_for_orthomcl (72)
[00/776e43] Submitted process > blast_for_orthomcl (73)
[03/527cd7] Submitted process > blast_for_orthomcl (74)
[37/533e93] Submitted process > blast_for_orthomcl (75)
[37/8c055a] Submitted process > blast_for_orthomcl (76)
[fd/d05c49] Submitted process > blast_for_orthomcl (77)
[be/cd29af] Submitted process > blast_for_orthomcl (78)
[df/ac7190] Submitted process > blast_for_orthomcl (79)
[e7/e2a317] Submitted process > blast_for_orthomcl (80)
[9e/f02cdd] Submitted process > blast_for_orthomcl (81)
[24/92a454] Submitted process > blast_for_orthomcl (82)
[e6/98ca1b] Submitted process > blast_for_orthomcl (83)
[0a/e43545] Submitted process > blast_for_orthomcl (84)
[6f/802280] Submitted process > blast_for_orthomcl (85)
[61/d168db] Submitted process > blast_for_orthomcl (86)
[ce/6b1cc1] Submitted process > blast_for_orthomcl (87)
[97/881d8a] Submitted process > blast_for_orthomcl (88)
[ef/33702a] Submitted process > blast_for_orthomcl (89)
[f4/7999d1] Submitted process > blast_for_orthomcl (90)
[7d/b07660] Submitted process > blast_for_orthomcl (91)
[2e/a08bd3] Submitted process > blast_for_orthomcl (92)
[63/bdc3b7] Submitted process > blast_for_orthomcl (93)
[e0/56dada] Submitted process > blast_for_orthomcl (94)
[b0/2451bc] Submitted process > blast_for_orthomcl (95)
[48/eaf642] Submitted process > blast_for_orthomcl (96)
[3c/619bc6] Submitted process > blast_for_orthomcl (97)
[70/e50154] Submitted process > blast_for_orthomcl (98)
[2d/2f2058] Submitted process > blast_for_orthomcl (99)
[0e/423e20] Submitted process > blast_for_orthomcl (100)
[a9/9980c0] Submitted process > blast_for_orthomcl (101)
[07/57536c] Submitted process > blast_for_orthomcl (102)
[d5/0d3426] Submitted process > blast_for_orthomcl (103)
[88/171212] Submitted process > blast_for_orthomcl (104)
[43/0d5dac] Submitted process > blast_for_orthomcl (105)
[a4/f87a16] Submitted process > blast_for_orthomcl (106)
[f3/2c765a] Submitted process > blast_for_orthomcl (107)
[65/173a40] Submitted process > blast_for_orthomcl (108)
[bd/645cba] Submitted process > blast_for_orthomcl (109)
[7a/e462a5] Submitted process > blast_for_orthomcl (110)
[9b/289107] Submitted process > blast_for_orthomcl (111)
[8f/47beb4] Submitted process > blast_for_orthomcl (112)
[82/2e1c9f] Submitted process > blast_for_orthomcl (113)
[db/4f6b4a] Submitted process > blast_for_orthomcl (114)
[ab/508455] Submitted process > blast_for_orthomcl (115)
[24/e34960] Submitted process > blast_for_orthomcl (116)
[4e/ee3276] Submitted process > blast_for_orthomcl (117)
[41/202071] Submitted process > blast_for_orthomcl (118)
[d0/2b9bb7] Submitted process > blast_for_orthomcl (119)
[d4/1bfcbe] Submitted process > blast_for_orthomcl (120)
[90/2153e8] Submitted process > blast_for_orthomcl (121)
[d7/5d4b87] Submitted process > blast_for_orthomcl (122)
[dd/5c7f74] Submitted process > blast_for_orthomcl (123)
[d5/ba1e7f] Submitted process > blast_for_orthomcl (124)
[b8/d43cfc] Submitted process > blast_for_orthomcl (125)
[c2/2c5296] Submitted process > blast_for_orthomcl (126)
[3c/a0ddac] Submitted process > blast_for_orthomcl (127)
[1f/009f42] Submitted process > blast_for_orthomcl (128)
[02/d1a130] Submitted process > blast_for_orthomcl (129)
[09/af9151] Submitted process > blast_for_orthomcl (130)
[93/f460fd] Submitted process > blast_for_orthomcl (131)
[7d/5e339b] Submitted process > blast_for_orthomcl (132)
[01/ac59e8] Submitted process > blast_for_orthomcl (133)
[49/e97390] Submitted process > blast_for_orthomcl (134)
[31/66cd91] Submitted process > blast_for_orthomcl (135)
[f5/964d41] Submitted process > blast_for_orthomcl (136)
[4d/aa154b] Submitted process > blast_for_orthomcl (137)
[52/a3509e] Submitted process > blast_for_orthomcl (138)
[7a/dd67a3] Submitted process > blast_for_orthomcl (139)
[e9/f11387] Submitted process > blast_for_orthomcl (140)
[20/b7ba70] Submitted process > blast_for_orthomcl (141)
[88/1da0b2] Submitted process > blast_for_orthomcl (142)
[c9/18ec59] Submitted process > blast_for_orthomcl (143)
[59/47e6f5] Submitted process > blast_for_orthomcl (145)
[b3/55c8ee] Submitted process > blast_for_orthomcl (144)
[6b/c7d82f] Submitted process > blast_for_orthomcl (146)
[c8/c9f4d6] Submitted process > blast_for_orthomcl (147)
[a9/28b8cf] Submitted process > blast_for_orthomcl (148)
[1d/c9d6b3] Submitted process > blast_for_orthomcl (149)
[11/fc0efb] Submitted process > blast_for_orthomcl (150)
[ab/9f7b15] Submitted process > blast_for_orthomcl (151)
[ea/7455ce] Submitted process > blast_for_orthomcl (152)
[50/525e92] Submitted process > blast_for_orthomcl (153)
[45/610d39] Submitted process > blast_for_orthomcl (154)
[7a/af23cc] Submitted process > blast_for_orthomcl (155)
[73/9bc5c8] Submitted process > blast_for_orthomcl (156)
[2e/af27a5] Submitted process > blast_for_orthomcl (157)
[bb/23fa6f] Submitted process > blast_for_orthomcl (158)
[ee/92ead1] Submitted process > blast_for_orthomcl (159)
[a5/7e3c57] Submitted process > blast_for_orthomcl (160)
[c8/7b201c] Submitted process > blast_for_orthomcl (161)
[58/3d1f3a] Submitted process > blast_for_orthomcl (162)
[11/6512d2] Submitted process > blast_for_orthomcl (163)
[89/83a2ef] Submitted process > blast_for_orthomcl (164)
[31/0bbec5] Submitted process > blast_for_orthomcl (165)
[62/0a563d] Submitted process > blast_for_orthomcl (166)
[df/9fd5c8] Submitted process > blast_for_orthomcl (167)
[80/0e8048] Submitted process > blast_for_orthomcl (168)
[f6/f3c43e] Submitted process > blast_for_orthomcl (169)
[b6/d0a0d7] Submitted process > blast_for_orthomcl (170)
[11/e117c6] Submitted process > blast_for_orthomcl (171)
[4b/7cae98] Submitted process > blast_for_orthomcl (172)
[80/6892fa] Submitted process > blast_for_orthomcl (173)
[6c/032015] Submitted process > blast_for_orthomcl (174)
[32/ac6b8c] Submitted process > blast_for_orthomcl (175)
[bd/72bea2] Submitted process > blast_for_orthomcl (176)
[e2/44244f] Submitted process > blast_for_orthomcl (177)
[2c/fd19f4] Submitted process > blast_for_orthomcl (178)
[06/0dbea5] Submitted process > blast_for_orthomcl (179)
[b9/ff0421] Submitted process > blast_for_orthomcl (180)
[ad/c624da] Submitted process > blast_for_orthomcl (181)
[ba/4b77f1] Submitted process > blast_for_orthomcl (182)
[a3/2d8079] Submitted process > blast_for_orthomcl (183)
[6a/ba1a68] Submitted process > blast_for_orthomcl (184)
[cf/32662a] Submitted process > blast_for_orthomcl (185)
[7c/f8e3b0] Submitted process > blast_for_orthomcl (186)
[ce/ea73eb] Submitted process > blast_for_orthomcl (187)
[a4/e9cc3a] Submitted process > blast_for_orthomcl (188)
[a2/57768f] Submitted process > blast_for_orthomcl (189)
[8c/e58944] Submitted process > blast_for_orthomcl (190)
[c0/fe9ad4] Submitted process > blast_for_orthomcl (191)
[21/2871aa] Submitted process > blast_for_orthomcl (192)
[ac/72c6fa] Submitted process > blast_for_orthomcl (193)
[14/8936ad] Submitted process > blast_for_orthomcl (194)
[8c/e6cb2b] Submitted process > blast_for_orthomcl (195)
[05/98b282] Submitted process > blast_for_orthomcl (196)
[b0/bec015] Submitted process > blast_for_orthomcl (197)
[dd/85f902] Submitted process > blast_for_orthomcl (198)
[0d/ac44e0] Submitted process > blast_for_orthomcl (199)
[08/f590d8] Submitted process > blast_for_orthomcl (200)
[be/680173] Submitted process > blast_for_orthomcl (201)
[49/74cb91] Submitted process > blast_for_orthomcl (202)
[39/f275eb] Submitted process > blast_for_orthomcl (203)
[e7/a41008] Submitted process > blast_for_orthomcl (204)
[66/50eba1] Submitted process > blast_for_orthomcl (205)
[16/70c4ae] Submitted process > blast_for_orthomcl (206)
[e8/7e8ff6] Submitted process > blast_for_orthomcl (207)
[49/ae991b] Submitted process > blast_for_orthomcl (208)
[cf/e6266b] Submitted process > blast_for_orthomcl (209)
[9d/f4eabb] Submitted process > blast_for_orthomcl (210)
[8a/280eb1] Submitted process > blast_for_orthomcl (211)
[61/619102] Submitted process > blast_for_orthomcl (212)
[33/1ca478] Submitted process > blast_for_orthomcl (213)
[8e/e9e2c0] Submitted process > blast_for_orthomcl (214)
[df/68231a] Submitted process > blast_for_orthomcl (215)
[d3/9f3215] Submitted process > blast_for_orthomcl (216)
[58/0b4f2f] Submitted process > blast_for_orthomcl (217)
[50/c88903] Submitted process > blast_for_orthomcl (218)
[f4/1ea3bd] Submitted process > blast_for_orthomcl (219)
[eb/84e9cf] Submitted process > blast_for_orthomcl (220)
[17/0ac490] Submitted process > blast_for_orthomcl (221)
[97/102c67] Submitted process > blast_for_orthomcl (222)
[01/c9f8a4] Submitted process > blast_for_orthomcl (223)
[34/b864bf] Submitted process > blast_for_orthomcl (224)
[4b/587146] Submitted process > blast_for_orthomcl (225)
[33/e30b12] Submitted process > blast_for_orthomcl (226)
[9d/bc2f78] Submitted process > blast_for_orthomcl (227)
[fc/f86a0b] Submitted process > blast_for_orthomcl (228)
[ee/fb241d] Submitted process > blast_for_orthomcl (229)
[1e/dca81f] Submitted process > blast_for_orthomcl (230)
[ed/4b5d11] Submitted process > blast_for_orthomcl (231)
[2f/c5ab81] Submitted process > blast_for_orthomcl (232)
[22/6d4d97] Submitted process > blast_for_orthomcl (233)
[8c/542c95] Submitted process > blast_for_orthomcl (234)
[8d/5161df] Submitted process > blast_for_orthomcl (235)
[30/50f69a] Submitted process > blast_for_orthomcl (236)
[1a/1f40a3] Submitted process > blast_for_orthomcl (237)
[6a/f2e48a] Submitted process > blast_for_orthomcl (238)
[f5/7c761a] Submitted process > blast_for_orthomcl (239)
[96/22c455] Submitted process > blast_for_orthomcl (240)
[09/e378ba] Submitted process > blast_for_orthomcl (241)
[0c/a5aa0b] Submitted process > blast_for_orthomcl (242)
[ba/a5e2e9] Submitted process > blast_for_orthomcl (243)
[4e/a9b0b2] Submitted process > blast_for_orthomcl (244)
[ce/9efd0b] Submitted process > blast_for_orthomcl (245)
[4c/ee3b78] Submitted process > blast_for_orthomcl (246)
[17/da4df7] Submitted process > pfam_to_gff3 (1)
[79/a35d77] Submitted process > parse_blastout_for_orthomcl (1)
[cf/4644e7] Submitted process > run_orthomcl (1)
[ac/bb23c0] Submitted process > annotate_orthologs (1)
[1f/026dd4] Submitted process > annotate_pfam (1)
[61/767d75] Submitted process > make_distribution_gaf (1)
[a2/b8ff58] Submitted process > make_distribution_gff (1)
[f4/fe75e4] Submitted process > make_genelist (1)
[75/a0701a] Submitted process > make_genome_stats (1)
[e9/2466c9] Submitted process > add_products_to_protein_fasta (1)
[46/9a7853] Submitted process > merge_gff3_for_gff3toembl (1)
[37/73ad0b] Submitted process > make_report (1)
[df/c88318] Submitted process > reference_compare (1)
[21/82ec5e] Submitted process > make_circos_inputs (1)
[31/13f898] Submitted process > make_embl (1)
[b4/745727] Submitted process > make_tree (1)
[38/8f0755] Submitted process > circos_run_chrs (5A_C_albicans_SC5314)
[48/be82e0] Submitted process > circos_run_chrs (RA_C_albicans_SC5314)
[cc/9c3364] Submitted process > circos_run_chrs (2A_C_albicans_SC5314)
[64/5b1fba] Submitted process > circos_run_chrs (1A_C_albicans_SC5314)
[55/fdeea3] Submitted process > circos_run_chrs (6A_C_albicans_SC5314)
[d7/ca8298] Submitted process > circos_run_chrs (3A_C_albicans_SC5314)
[1c/50ba29] Submitted process > circos_run_chrs (7A_C_albicans_SC5314)
[86/c3687f] Submitted process > circos_run_chrs (4A_C_albicans_SC5314)
The parameters you have chosen for your FungiDB-60_CdubliniensisCD36_Genome.fasta vs. Candida albicans SC5314 - in chromosomes run are:
Pseudochromosomes
Protein evidence
Transfer tool RATT
RATT transfer type Species
SNAP
Max gene length 50000
Score threshold 0.4
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

Ss results

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 2.0 format) is also provided for custom analyses.

Ss venn

Ss tree

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

Ss validator

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.