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Protocols

SmartBlast specifications

Information


Unique identifier OMICS_16325
Name SmartBlast
Interface Web user interface
Restrictions to use None
Input data One protein accession.
Input format FASTA
Computer skills Basic
Stability Stable
Maintained No

SmartBlast citations

 (11)
library_books

Gene Expression of Pneumocystis murina after Treatment with Anidulafungin Results in Strong Signals for Sexual Reproduction, Cell Wall Integrity, and Cell Cycle Arrest, Indicating a Requirement for Ascus Formation for Proliferation

2018
PMCID: 5923105
PMID: 29463544
DOI: 10.1128/AAC.02513-17

[…] fold change in p. murina gene expression between infected, untreated mice and mice treated with anidulafungin for 2 weeks., e value of sequence homology to the known genes as reported by the ncbi smartblast tool., sequence identity (percentage) to the known genes and organisms. organism abbreviations: sp, schizosaccharomyces pombe; sc, saccharomyces cerevisiae; pc, pneumocystis carinii. hp, […]

library_books

De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

2018
PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w

[…] file ., genes and transcripts for each examined genome were identified by a tblastn search (e-value cut-off of 10−5) using the sequencerserver software. this was followed by a reciprocal blast using smartblast, to confirm their identity., conserved protein domains used to identify the corresponding orthologous proteins within tunicate genomes are found in table ., sequences were aligned […]

library_books

Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep sea symbiotic Spiroplasma

2018
PMCID: 5861454
PMID: 29390076
DOI: 10.1093/nar/gky045

[…] the genome were searched using trnascan (). the genes for potential trna posttranscriptional modifications and their targets were predicted with trnamodpred (). phylogeny-based filtration and ncbi smartblast were performed to examine the output of trnamodpred., the codon usage bias of the cdss was evaluated by measurement of relative synonymous codon usage (rscu) and codon adaptation index […]

library_books

Database resources of the National Center for Biotechnology Information

2017
PMCID: 5753372
PMID: 29140470
DOI: 10.1093/nar/gkx1095

[…] algorithm works best for queries longer than 50 residues, and is limited to queries of <10 000 residues. access to quickblastp is provided as an algorithm option on the main blastp web page., the smartblast service quickly returns the most similar proteins to a query, and was updated in 2017 to prioritize matching proteins to the ‘landmark’ database that contains proteomes from 26 […]

call_split

A Journey across Genomes Uncovers the Origin of Ubiquinone in Cyanobacteria

2017
PMCID: 5714133
PMID: 29106540
DOI: 10.1093/gbe/evx225
call_split See protocol

[…] of this method was developed and showed high correlation with the results of genomic chimaerism obtained previously (; ). this method is based on the computation of the top five hits obtained with smartblast [https://blast.ncbi.nlm.nih.gov/smartblast/] for about 100 proteins essential for membrane and energy metabolism (the list of these proteins will be made available upon request). […]

library_books

TaFlo2 A1, an ortholog of rice Flo2, is associated with thousand grain weight in bread wheat (Triticum aestivum L.)

2017
PMCID: 5644068
PMID: 29037166
DOI: 10.1186/s12870-017-1114-3

[…] were predicted using softberry software (http://www.softberry.com/berry.phtml). the predicted taflo2 protein was blasted both in the ncbi smart blast system (http://blast.st-va.ncbi.nlm.nih.gov/smartblast) to search for homologous proteins and in the ncbi cd system (https://www.ncbi.nlm.nih.gov/structure/cdd/wrpsb.cgi) to search for conserved domains., to select potential candidate taflo2 […]


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