BLAST Search

Search for one or more of your sequences (using BLAST). First pick a query type (nucleotide or protein). You will be able to set search parameters on the next page. Choose the appropriate program based on the Query type and Target database type. Please click on the program name to view the search form. Video Tutorial

Query Type Database Type BLAST Program
Nucleotide Nucleotide blastn: Search a nucleotide database using a nucleotide query.
Protein blastx: Search protein database using a translated nucleotide query.
Protein Nucleotide tblastn: Search translated nucleotide database using a protein query.
Protein blastp: Search protein database using a protein query.
BLAST References
1. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403–410.
2. Camacho,C., Coulouris,G., Avagyan,V., Ma,N., Papadopoulos,J., Bealer,K., and Madden T.L. (2009) BLAST+: architecture and applications. BMC Bioinformatics, 10:421, doi: 10.1186/1471-2105-10-421.
Database Name Source
=== Peptides ===  
All Gossypium Proteins A Combination of Proteins from NCBI, UniprotKB and Gossypium whole genome sequensing projects
GenBank Gossypium NR Sequences NCBI GenBank Gossypium NR Sequences, 2019-03-01
UniProtKB Gossypium Sequences UniProtKB Gossypium Sequences,  2019-03-01
=== Nucleotides ===  
GenBank Gossypium Sequences NCBI GenBank Gossypium NT, EST, and GSS Sequences (WGS and RefSeq not included), 2019-03-01
CottonGen Markers CottonGen RAD, RFLP, SSR, SNP marker sequences, 2018-11-29
CottonGen RefTrans Gossypium species specific assemblies of filtered RNA-seq reads and unigenes performed by CottonGen, 2016-11-14
Gossypium Gene, CDS and Unigenes Gossypium genes, CDS, and unigenes from NCBI, PlantGDB, TIGR, cotton community, and whole genome sequence projects
=== Whole Genomes ===  
Gossypium hirsutum CRI-ZM24 v1, a1 G. hirsutum (AD1) Genome CRI assembly v1 & annotation a1 [ZM24], 2019-09 new
Gossypium hirsutum CRI-TM1 v1, a1 G. hirsutum (AD1) Genome CRI assembly v1 & annotation a1 [TM-1], 2019-09 new
Gossypium hirsutum ZJU v2.1, a1 G. hirsutum (AD1) Genome ZJU assembly v2.1 & annotation a1.0, [TM-1], 2019-03-18
Gossypium hirsutum HAU v1.1, a1.1 G. hirsutum (AD1) Genome HAU assembly v1.1 & annotation a1.1, [TM-1], 2019-03-16
Gossypium hirsutum HAU v1, a1 G. hirsutum (AD1) Genome HAU assembly v1.0 & annotation a1.0, [TM-1], 2018-12-03
Gossypium hirsutum JGI v1, a1.1 G. hirsutum (AD1) Genome JGI assembly v1.0 & annotation a1.1, [TM-1], 2017-09-04
Gossypium hirsutum NBI v1.1, a1.1 G. hirsutum (AD1) Genome NAU-NBI assembly v1.1 & annotation a1.1, [TM-1], 2015-04-20
Gossypium hirsutum BGI v1, a1 G. hirsutum (AD1) Genome CGP-BGI assembly v1.0 & annotation a1, [TM-1], 2015-04-20
Gossypium barbadense ZJU v1.1, a1 G. barbadense (AD2) Genome ZJU assembly v1.1 & annotation a1, [Hai-7124], 2019-03-18
Gossypium barbadense HAU v2, a1 G. barbadense (AD2) Genome HAU assembly v2.0 & annotation a1, [3-79], 2018-12-03
Gossypium barbadense HAU v1, a1 G. barbadense (AD2) Genome HAU assembly v1.0 & annotation a1, [3-79], 2016-03-25
Gossypium mustelinum JGI v1.1, a1.1 G. mustelinum (AD4) Genome JGI assembly v1.1 & annotation a1.1, [unknown], 2019-11 new
Gossypioides kirkii ISU v3, a3 Gossypioides kirkii Genome ISU assembly v3 & annotation a3, [JFW-EA], 2019-09 new
Gossypium arboreum CRI v1, a1 G. arboreum (A2) Genome CRI Updated assembly v1.0 & annotation a1.0, [Shi Xi Ya 1], 2019-03-01
Gossypium arboreum NCGR contigs & scaffolds only G. arboreum (A2) Genome NCGR shotgun sequences downloaded from NCBI, [AKA 8401], 2015-01-23
Gossypium arboreum BGI v2, a1 G. arboreum (A2) Genome BGI assembly v2.0 & annotation a1.0, [Shi Xi Ya 1], 2014-05-31
Gossypium raimondii NSF v1, a1 G. raimondii (D5) Genome NSF assembly v1.0 & annotaion a1.0, [D5-4], 2019-08
Gossypium raimondii JGI v2, a2.1 G. raimondii (D5) genome JGI assembly v2.0 annotation a2.1), [germplasm unknown], 2013-02-18
Gossypium raimondii BGI v1, a1 G. raimondii (D5) genome BGI-CGP draft assembly & annotation a1.0, [D5-3], 2012-01-11
Gossypium turneri NSF v1, a2 G. turneri (D10) genome NSF assembly v1.0 & annotation a2, [D10-3], 2019-08
Gossypium australe CRI v1.1, a1.1 G. australe (G2) genome CRI assembly v1.1 & annotation a1.1, [PA-1801], 2019-11 new