PSI-Search protocols

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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 in pipelines

 (3)
2017
PMCID: 5438488
PMID: 28526057
DOI: 10.1186/s13062-017-0184-3

[…] 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 […]

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

[…] 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 […]

2009
PMCID: 2707011
PMID: 19606221
DOI: 10.1371/journal.pone.0006260

[…] over a vast number of organisms., tectonin domain containing proteins were identified using domain search on the smart database , . a position-specific iterated search using the primary sequence on psi-search on the embl server was performed using gbp as the query sequence. related sequences were chosen after 2 iterations of psi-search. hits were put through the smart prediction server […]


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PSI-Search in publications

 (8)
PMCID: 5438488
PMID: 28526057
DOI: 10.1186/s13062-017-0184-3

[…] 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 […]

PMCID: 4690856
PMID: 26633460
DOI: 10.3390/v7122932

[…] 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 […]

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

[…] 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 […]

PMCID: 4129151
PMID: 25165734
DOI: 10.1155/2014/186029

[…] 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 […]

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

[…] 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 […]


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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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