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Number of citations per year for the bioinformatics software tool CS-BLAST
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Protocols

CS-BLAST specifications

Information


Unique identifier OMICS_05170
Name CS-BLAST
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_05170
Name CS-BLAST
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Publication for CS-BLAST

CS-BLAST citations

 (22)
call_split

Sendai virus recruits cellular villin to remodel actin cytoskeleton during fusion with hepatocytes

2017
Mol Biol Cell
PMCID: 5739296
PMID: 29074568
DOI: 10.1091/mbc.E17-06-0400
call_split See protocol

[…] The conservation at each of the 46 threonine residues in villin was analyzed using the ConSeq () server. Homologues were retrieved from UNIREF90 using the CS-BLAST algorithm with three iterations, an E-value cutoff of 0.0001, and a minimum sequence identity of 25%. Sequences were then clustered at 90% sequence identity to remove any redundancy in the da […]

call_split

Dual role of starvation signaling in promoting growth and recovery

2017
PLoS Biol
PMCID: 5728490
PMID: 29236696
DOI: 10.1371/journal.pbio.2002039
call_split See protocol

[…] PHO84 homologs was established with ConSurf []. Starting from the PHO84 protein sequence (SGD) as input, multiple sequence alignment was built using MAFFT. The homologs were collected from UNIREF90. CS-BLAST was used for the homolog search algorithm, with search parameters of CSI-BLAST E-value of 0.0001, a maximal ID of 95%, and a minimal ID of 35%, and 3 iterations of CSI-BLAST. CSI-BLAST result […]

call_split

A Small Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage

2017
ACS Synth Biol
PMCID: 5696648
PMID: 28826208
DOI: 10.1021/acssynbio.7b00108
call_split See protocol

[…] A comprehensive database of LexA homologues was generated using the ConSurf Server Database, which utilizes CS-BLAST of the SWISS-PROT protein databank to calculate sequence homology and conservation of protein structures. LexA homologues were aligned and percent identity calculated using Jalview sequence a […]

library_books

A dynamic hydrophobic core orchestrates allostery in protein kinases

2017
Sci Adv
PMCID: 5384802
PMID: 28435869
DOI: 10.1126/sciadv.1600663

[…] The sequence conservation was plotted onto the protein structure using ConSurf-DB (, ). Initially, a CS-BLAST () search against the SWISS-PROT database was performed to obtain at least 50 unique hits. The list of collected homologs was subsequently filtered by coverage (minimum of 80%) and sequence i […]

library_books

Protein sequence similarity search acceleration using a heuristic algorithm with a sensitive matrix

2017
J Struct Funct Genomics
PMCID: 5274646
PMID: 28083762
DOI: 10.1007/s10969-016-9210-4

[…] s is restricted to proteins with structural information. One line of research has pursued incorporation of the sequence context into homology searches. Deviating from the form of substitution matrix, CS-BLAST deals with substitution probabilities in the form of a sequence profile computed based on nearby sequence context, by which significant sensitivity enhancement was achieved []. Implementation […]

call_split

Benchmarking the next generation of homology inference tools

2016
Bioinformatics
PMCID: 5013910
PMID: 27256311
DOI: 10.1093/bioinformatics/btw305
call_split See protocol

[…] enerated for the final benchmark dataset.For each protein pair evaluated, each pair was aligned (i.e. one protein used as database, one as query) using each of the profile-based homology search tools CS-BLAST (), HHSEARCH () and PHMMER () as well as the non-profile based NCBI-BLAST (), USEARCH/UBLAST () and FASTA () for comparison. All methods were run with default parameters where not otherwise n […]


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CS-BLAST institution(s)
Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universtät München, Munich, Germany

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