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 KOs largely meets the preferred needs of most scientists studying non-model organisms.
  
  We provide dozens of pre-built databases that can be downloaded here.
  Note: * these KOs in the database are KOs assigned to KEGG pathways and they are only a proportion of whole list of KOs.
  ** all KOs include KOs not assigned to KEGG pathways.
  
  We are collecting and constructing other databases such as genes of GO and PANTHER.

  Group	Species	Proteins*	KOs*	Filename*	Proteins**	KOs**	Filename**
  Eukaryotes	537	1,908,542	8,041	eukaryotes.tar.gz	3,950,549	15,302	eukaryotes_all_KOs.tar.gz
  Animals	250	1,126,598	6,723	animals.tar.gz	2,446,258	12,984	animals_all_KOs.tar.gz
  Plants	105	480,379	3,012	plants.tar.gz	926,166	6,363	plants_all_KOs.tar.gz
  Fungi	130	237,631	2,423	fungi.tar.gz	444,690	4,987	fungi_all_KOs.tar.gz
  Protists	51	64,058	2,696	protists.tar.gz	133,614	6,505	protists_all_KOs.tar.gz
  Mammals	66	378,311	5,622	mammals.tar.gz	689,252	11,078	mammals_all_KOs.tar.gz
  Birds	24	87,530	4,177	birds.tar.gz	208,153	9,718	birds_all_KOs.tar.gz
  Reptiles	12	62,677	4,342	reptiles.tar.gz	153,373	10,113	reptiles_all_KOs.tar.gz
  Amphibians	3	20,880	4,207	amphibians.tar.gz	50,137	9,715	amphibians_all_KOs.tar.gz
  Fishes	39	273,691	4,308	fishes.tar.gz	783,801	10,510	fishes_all_KOs.tar.gz
  Arthropods	72	196,277	3,541	arthropods.tar.gz	455,750	8,723	arthropods_all_KOs.tar.gz
  Nematodes	6	13,379	2,324	nematodes.tar.gz	30,128	5,260	nematodes_all_KOs.tar.gz

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

• If you want us to build databases of organisms or group (e.g., mammals + birds) of organisms in the following table, please send us the list of organisms or groups CONTACT
  
  

• The following 6 databases are used for the assessment of Seq2Fun with mouse, chicken and zebrafish 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