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Protocols

BLASTP specifications

Information


Unique identifier OMICS_00991
Name BLASTP
Alternative name Standard Protein BLAST
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtools


  • DELTA-BLAST
  • PHI-BLAST
  • PSI-BLAST

Maintainer


  • person_outline Stephen Altschul

Publications for Standard Protein BLAST

library_books

PSI-BLAST tutorial.

2007 Methods Mol Biol
PMCID: 4781153
PMID: 17993673

BLASTP citations

 (11286)
call_split

Bat Caliciviruses and Human Noroviruses Are Antigenically Similar and Have Overlapping Histo Blood Group Antigen Binding Profiles

2018
MBio
PMCID: 5964351
DOI: 10.1128/mBio.00869-18
call_split See protocol

[…] the basic local alignment search tool (BLAST) from the National Center for Biotechnology Information (NCBI) (). BLAST searches were conducted at the amino acid level using the protein-protein BLAST (blastp) function to query nonredundant protein sequences. […]

call_split

Comparative genomic analysis of Acinetobacter spp. plasmids originating from clinical settings and environmental habitats

2018
Sci Rep
PMCID: 5958079
PMID: 29773850
DOI: 10.1038/s41598-018-26180-3
call_split See protocol

[…] accomplished using the CONSED software package. Complete closed replicons were automatically annotated by the genome annotation system GenDB and manually curated. Genes were annotated using the best BLASTP hit at the National Center for Biotechnology Information (NCBI) database (http://www.ncbi.nlm.nih.gov/). Replicon sequences were submitted to GenBank and registered under Bioproject ID PRJEB221 […]

library_books

AID/APOBEC like cytidine deaminases are ancient innate immune mediators in invertebrates

2018
Nat Commun
PMCID: 5956068
PMID: 29769532
DOI: 10.1038/s41467-018-04273-x

[…] Sequence comparisons to the sea urchin genome were done using BLAST, BLASTP, or BLASTN at https://blast.ncbi.nlm.nih.gov/Blast.cgi or www.echinobase.org using either standard parameters or with low complexity filter turned off. Multiple sequence alignments were perform […]

call_split

Endocytosis mediated siderophore uptake as a strategy for Fe acquisition in diatoms

2018
Sci Adv
PMCID: 5955625
PMID: 29774236
DOI: 10.1126/sciadv.aar4536
call_split See protocol

[…] The ISIP1 protein sequence (Phatr3_J55031) was used as the seed sequence for BLASTp analysis against a curated library comprising all protein sequences in UniRef, the MMETSP (), and all additional sequences hosted on the JGI portal. This composite database, described by Dorrel […]

call_split

Genomic and functional characterisation of IncX3 plasmids encoding blaSHV 12 in Escherichia coli from human and animal origin

2018
Sci Rep
PMCID: 5955891
PMID: 29769695
DOI: 10.1038/s41598-018-26073-5
call_split See protocol

[…] des version 3.7.1) for Illumina-derived reads and then manually curated to close the gaps. Putative open reading frames (ORFs) were identified by RAST version 2.0 and manually curated when necessary. BLASTP analyses of the putative ORFs against the NCBI non-redundant proteins (NR) database, Pfam, and Interpro scan were used to assess their putative functions by identification of structural feature […]

library_books

Multiple origins of green blood in New Guinea lizards

2018
Sci Adv
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] bp (42,543,058 to 17,007,264,440) per sample. Filtered reads were assembled into contigs using Trinity (). To check for contamination, all contigs were aligned to the nonredundant protein database by BLASTP with an e value cutoff of 1 × 10−6 and checked for best hits to squamate reptiles. We also performed an all-versus-all blast search on the assemblies and removed six individuals that had recipr […]

Citations

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