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Protocols

PSI-Search specifications

Information


Unique identifier OMICS_14459
Name PSI-Search
Interface Web user interface, Application programming interface
Restrictions to use None
Input data A protein sequence
Input format GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP, UniProtKB/Swis-Prot
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline William Pearson

Information


Unique identifier OMICS_14459
Name PSI-Search
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A protein sequence
Input format GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP, UniProtKB/Swis-Prot
Operating system Unix/Linux
Programming languages Perl
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline William Pearson

Publications for PSI-Search

PSI-Search citations

 (10)
library_books

Recognition of a structural domain (RWDBD) in Gcn1 proteins that interacts with the RWD domain containing proteins

2017
Biol Direct
PMCID: 5438488
PMID: 28526057
DOI: 10.1186/s13062-017-0184-3

[…] tify Gcn1 proteins in other eukaryotic organisms, the yeast Gcn1 sequence (Uniprot ID: P33892) was searched against UniprotKB Eukaryota database [] which contains more than 22 million sequences using PSI-Search [, ] at an E-value threshold of 0.000001, sequence identity cut-off of 25%, three iterations and query coverage cut-off of 75%. At each iteration putative, predicted and uncharacterized seq […]

library_books

Programmatic access to bioinformatics tools from EMBL EBI update: 2017

2017
Nucleic Acids Res
PMCID: 5570243
PMID: 28431173
DOI: 10.1093/nar/gkx273

[…] makes it possible to analyze detailed usage with common analytic tools. At present, tools include sequence similarity search services (https://www.ebi.ac.uk/Tools/sss/) such as BLAST (), FASTA () and PSI-Search (), multiple sequence alignment tools (https://www.ebi.ac.uk/Tools/msa/) such as Clustal Omega (), MAFFT () and KAlign (), and other sequence analysis tools (https://www.ebi.ac.uk/Tools/pfa […]

library_books

Incomplete LPS Core Specific Felix01 Like Virus vB_EcoM_VpaE1

2015
Viruses
PMCID: 4690856
PMID: 26633460
DOI: 10.3390/v7122932

[…] Open reading frames (ORFs) were predicted with Glimmer v2.02 [] and Geneious v5.5.6. []. Analysis of the genome sequence was performed using the Fasta-Protein, Fasta-Nucleotide, Fasta-Genome, BLAST2, PSI-Search, Transeq, ClustalW2, (European Bioinformatics Institute, Hinxton, UK), programs, and tRNAscan-SE 1.21 [] was used to search for tRNAs. The complete genome sequence of vB_EcoM_VpaE1 was depo […]

library_books

Isolation and Characterization of vB_ArS ArV2 – First Arthrobacter sp. Infecting Bacteriophage with Completely Sequenced Genome

2014
PLoS One
PMCID: 4205034
PMID: 25333962
DOI: 10.1371/journal.pone.0111230

[…] ://nbc11.biologie.uni-kl.de) and Geneious v5.5.6. (Société Geneious, Colombes, France). Analysis of the genome sequence was performed using the Fasta-Protein, Fasta-Nucleotide, Fasta- Genome, BLAST2, PSI-Search, Transeq, ClustalW2, (http://www.ebi.ac.uk), HHsearch1.6 (http://toolkit.tuebingen.mpg. de/hhpred), COMA (http://bioinformatics.ibt.lt:8085/coma), Sequence editor (http://www.fr33.net/seqed […]

library_books

Molecular Phylogeny and Predicted 3D Structure of Plant beta D N Acetylhexosaminidase

2014
Sci World J
PMCID: 4129151
PMID: 25165734
DOI: 10.1155/2014/186029

[…] unctional prediction, active site information, and mechanism of action.In the present work, first we identified the 83 homologous sequences of β-N-acetyl-D-hexosaminidase in GenBank by the NCBI BLAST-PSI search. We did multiple sequence alignments and reconstructed the phylogenetic tree. Secondly, in order to initiate structural studies of this enzyme, we performed sequence alignment and 3D-struct […]

library_books

Adjusting scoring matrices to correct overextended alignments

2013
Bioinformatics
PMCID: 3834790
PMID: 23995390
DOI: 10.1093/bioinformatics/btt517

[…] asts with traditional false negatives, where the homology is missed altogether. In the traditional case, the reduced sensitivity of pairwise sequence comparisons compared with model-based (PSI-BLAST, PSI-SEARCH, HMMER) or structure-based methods is well recognized (). Incomplete alignments are another example of inadequate alignment sensitivity.Overextension, while recognized in pairwise genomic a […]

Citations

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PSI-Search institution(s)
Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, USA; European Bioinformatics Institute, EMBL Outstation, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
PSI-Search funding source(s)
This research was supported by the National Library of Medicine (NIH grant LM04969); European Molecular Biology Laboratory; and European Commission Research Infrastructures of the FP7 [grant agreement number 226073 SLING (Integrating Activity)].

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