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. 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.

Description and source of BLAST databases

Database Name Source
NCBI ESTs Species specific ESTs from NCBI dbEST, downloaded 6/14/17
Unigene v1 Species specific assemblies of NCBI dbEST data performed by CGD
CGD RefTrans v1 Species specific assemblies of filtered RNA-seq reads and unigenes performed by CGD
Citrus clementina cv. Clemenules v0.9 genome Previous version of JGI assembly
Citrus clementina cv. Clemenules v1.0 genome Most current JGI assembly, Wu et al. 2014
Citrus sinensis cv. Ridge Pineapple v1.0 genome Previous version of JGI assembly
Citrus sinensis cv. Ridge Pineapple v1.1 genome Most current JGI assembly, Wu et al. 2014
Citrus sinensis cv. Valencia v1.0 genome Chromosome level HZAU assembly, Xu et al. 2013
Citrus maxima (C. grandis) v1.0 genome Chromosome level HZAU assembly, Wang et al. 2017
Citrus ichangensis (C. cavaleriei) v1.0 genome Draft level HZAU assembly, Wang et al. 2017
Citrus medica v1.0 genome Draft level HZAU assembly, Wang et al. 2017
Atalantia buxifolia v1.0 genome Draft level HZAU assembly, Wang et al. 2017
Citrus reticulata v1.0 genome Draft level HZAU assembly, Wang et al. 2018
Poncirus trifoliata v1.3.1 genome JGI assembly, Peng et al. 2020
Fortunella hindsii v1.0 genome Draft level HZAU assembly, Zhu et al. 2019
Citrus aurantifolia transcriptome Transcripts from HLB-infected/non-infected leaves, Arce-Leal et al, 2020
Citrus limon v1.0 genome Primary and Alternative assemblies, Di Guardo et al, 2021
Citrus australasica CRC3672 v1.0 genome Primary and Alternate assemblies, Singh et al.
Citrus glauca CRC3463 v1.0 genome Primary and Alternate assemblies, Singh et al.
Citrus inodora CRC3784 v1.0 genome Primary and Alternate assemblies, Singh et al.
Ca. Liberibacter asiaticus genomes Complete genomes downloaded from NCBI
Ca. Liberibacter africanus genomes Complete genomes downloaded from NCBI
Ca. Liberibacter americanus genomes Complete genomes downloaded from NCBI
Ca. Liberibacter solanacearum genomes Complete genomes downloaded from NCBI
Liberibacter crescens genomes Complete genomes downloaded from NCBI