Seq2Fun Databases

• For most non-model organisms, biological understanding of study outcomes is limited to protein-coding genes with functional annotations such as KEGG pathways, Gene Ontology or PANTHER classification system. Therefore, developing Seq2Fun database to focus on functionally annotated genes such as, protein-coding genes, GOs and KOs largely meets the preferred needs of most scientists studying non-model organisms.
  
  We provide dozens (~30) of pre-built databases that can be downloaded here (then click Tab of "Without a Reference Transcriptome").
  Note: the ortholog includes all genes (including genes are not orthology with any other genes) from that groups of organisms.
  Groups of organisms can be download from here.
  
  The definition of a core ortholog is that its frequency in the group >= 0.90. This is in consistent with BUSCO
  Note: * frequency >= 0.85; ** frequency >= 0.80;

  Group	Species	Proteins	Ortholog	Core ortholog	Filename	Date
  Algae	14	155495	38334	1521	algae.tar.gz	07-11-2022
  alveolates	21	207674	51205	1132	alveolates.tar.gz	07-11-2022
  amoebozoa	7	81844	22114	1165	amoebozoa.tar.gz	07-11-2022
  amphibians	3	75261	17186	13925	amphibians.tar.gz	07-11-2022
  animals	370	7150735	270089	1512	animals.tar.gz	07-11-2022
  apicomplexans	18	93576	14632	1091	apicomplexans.tar.gz	07-11-2022
  arthropods	119	1727651	113673	5106	arthropods.tar.gz	07-11-2022
  ascomycetes	100	904642	98151	2799	ascomycetes.tar.gz	07-11-2022
  basidiomycetes	33	363997	56935	2453	basidiomycetes.tar.gz	07-11-2022
  birds	31	482205	22397	11761	birds.tar.gz	07-11-2022
  cnidarians	9	203000	24003	5547	cnidarians.tar.gz	07-11-2022
  crustaceans	7	154960	37407	5216	crustaceans.tar.gz	07-11-2022
  dothideomycetes	10	123200	28898	5567	dothideomycetes.tar.gz	07-11-2022
  eudicots	93	3180221	102679	8230	eudicots.tar.gz	07-11-2022
  euglenozoa	9	86483	12363	4638	euglenozoa.tar.gz	07-11-2022
  eurotiomycetes	20	196228	25710	4723	eurotiomycetes.tar.gz	07-11-2022
  fishes	64	1736572	43690	13248	fishes.tar.gz	07-11-2022
  flatworms	4	58181	17784	4237	flatworms.tar.gz	07-11-2022
  fungi	138	1278312	148080	2138	fungi.tar.gz	07-11-2022
  insects	101	1376824	70170	5971	insects.tar.gz	07-11-2022
  leotiomycetes	5	67865	21669	5707	leotiomycetes.tar.gz	07-11-2022
  mammals	94	1910363	47144	14776	mammals.tar.gz	07-11-2022
  mollusks	9	206905	35775	6726	mollusks.tar.gz	07-11-2022
  monocots	17	560027	43452	9611	monocots.tar.gz	07-11-2022
  nematodes	6	134093	35865	3280	nematodes.tar.gz	07-11-2022
  plants	127	3968027	162990	3485	plants.tar.gz	07-11-2022
  protists	52	660237	134452	602	protists.tar.gz	07-11-2022
  reptiles	20	384584	21725	12715	reptiles.tar.gz	07-11-2022
  saccharomycetes	36	195913	14873	3079	saccharomycetes.tar.gz	07-11-2022
  stramenopiles	8	119746	31582	567	stramenopiles.tar.gz	07-11-2022
  vertebrates	212	4588985	83704	8222	vertebrates.tar.gz	07-11-2022

  If you want to download the databases of Seq2Fun version 1, please click here.

• We fully support customer built database. See MANUAL 13. Custom built database.

• The following 8 databases are used for the assessment of Seq2Fun version 1 with mouse, chicken, zebrafish and roundworm datasets.
  The RNA-seq data can be download from here.

  Group	Proteins	KOs	Species	Filename
  Mammals_no_mouse	356,672	5,622	64	mammals_no_mouse.tar.gz
  Mouse	8,438	5,437	1	mouse.tar.gz
  Birds_no_chicken	81,576	4,176	23	birds_no_chicken.tar.gz
  Chicken	4,930	3,921	1	chicken.tar.gz
  Fishes_no_zebrafish	267,954	4,235	38	fishes_no_zebrafish.tar.gz
  Zebrafish	6,047	3,963	1	zebrafish.tar.gz
  Nematodes_no_roundworm	13,939	2,950	5	nematodes_no_worm.tar.gz
  Roundworm	3,081	2,391	1	worm.tar.gz