BLAST


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.

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 Reference
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.

Description and source of BLAST databases

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, downloaded 2017-08-25
UniProtKB Gossypium Sequences UniProtKB Gossypium Sequences,  downloaded 2017-08-25
=== Nucleotides ===  
GenBank Gossypium Sequences NCBI GenBank Gossypium NT, EST, and GSS Sequences (WGS and RefSeq not included), downloaded 2017-08-25
CottonGen Markers CottonGen RFLP, SSR, SNP marker sequences
CottonGen RefTrans Gossypium species specific assemblies of filtered RNA-seq reads and unigenes performed by CottonGen
Gossypium Gene, CDS and Unigenes Gossypium genes, CDS, and unigenes from NCBI, PlantGDB, TIGR, cotton community, and whole genoe sequence projects
=== Whole Genomes ===  
Gossypium arboreum BGI G. arboreum (A2) Genome BGI Assembly v2.0 & Annotation v1.0, [Shi Xi Ya 1], 2014-05-31
Gossypium arboreum NCGR contigs & scaffolds only G. arboreum (A2) Genome NCGR shotgun sequences downloaded from NCBI, [AKA 8401], 2015-01-23
Gossypium barbadense NBI G. barbadense (AD2) Genome HAU-SGI Assembly v1.0 & Annotation v1.0, [3-79] 2016-03-25
Gossypium hirsutum BGI G. hirsutum (AD1) Genome CGP-BGI Assembly v1.0 & Annotation v1.0, [TM-1] 2015-04-20
Gossypium hirsutum NBI G. hirsutum (AD1) Genome NAU-NBI Assembly v1.1 & Annotation v1.1, [TM-1] 2015-04-20
Gossypium raimondii BGI G. raimondii (D5) genome BGI-CGP draft assembly & annotation v1.0, [D5-3] 2012-01-11
Gossypium raimondii JGI G. raimondii (D5) genome JGI assembly v2.0 annotation v2.1), [germplasm unknown] 2013-02-18