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MSPcrunch specifications

Information


Unique identifier OMICS_23186
Name MSPcrunch
Alternative name MSPcrunch2
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data A gapped alignment, a graphical schematic and a tabular data.
Output format ASCII+ACE+EXBLX+SEQBL
Operating system Unix/Linux
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Erik Sonnhammer

Publication for MSPcrunch

MSPcrunch citations

 (7)
library_books

Zebrafish Rab5 proteins and a role for Rab5ab in nodal signalling

2015
Dev Biol
PMCID: 4294769
PMID: 25478908
DOI: 10.1016/j.ydbio.2014.11.007

[…] ere used as query sequence to identify zebrafish Ensembl predictions (Ensembl Zebrafish 19.3.2) (), which was based on the zebrafish genome assembly (Zv3)(), mRNAs and ESTs using WU-BLAST followed by MSPcrunch filtering (). We used a threshold of 60% identity as a human to zebrafish match. Zebrafish EST sequences were retrieved along with capillary sequence traces (http://www.ncbi.nlm.nih.gov/Trac […]

library_books

Analysis of Expressed Genes of the Bacterium ‘Candidatus Phytoplasma Mali’ Highlights Key Features of Virulence and Metabolism

2014
PLoS One
PMCID: 3984173
PMID: 24728201
DOI: 10.1371/journal.pone.0094391

[…] Mulberry dwarf phytoplasma proteins previously assigned to Tenericutes database entries were included in this study by BLASTP analysis using the annotated proteins of ‘Ca. P. mali’ as database . MSPcrunch was used for removal of hits exceeding the probability treshhold of 1e-5 and showing a sequence identity below 25% . […]

library_books

Tracing Lifestyle Adaptation in Prokaryotic Genomes

2012
Front Microbiol
PMCID: 3282942
PMID: 22363326
DOI: 10.3389/fmicb.2012.00048

[…] and their respective syntenies in an operon or genome-wide context. In combination with ORFeome based (ORF-to-ORF comparison on amino-acid level, a maximum of 20 similarity hits per ORF is permitted) MSPcrunch (Sonnhammer and Durbin, ) comparison format data files (pMSPs) created by the compACTor software and annotated GenBank files, the ACT (Carver et al., ) provides an excellent visualization pl […]

library_books

Gentle Masking of Low Complexity Sequences Improves Homology Search

2011
PLoS One
PMCID: 3242753
PMID: 22205972
DOI: 10.1371/journal.pone.0028819

[…] discriminate homologs with non-standard letter frequencies in a statistically powerful manner. blastz and lastz adjust alignment scores based on the entropy of their nucleotides . Among other tools, MSPcrunch filters alignments with biased letter frequencies , and hmmer3 uses a score correction for biased composition .To the best of our knowledge, all methods in this category consider only zero-o […]

library_books

Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae

2010
BMC Genomics
PMCID: 2897811
PMID: 20565991
DOI: 10.1186/1471-2164-11-393

[…] e present or absent potential orthologs within each genome.Potential paralogs were estimated using BLAST []. Deduced protein sets of the chromosomes were compared against themselves and filtered with MSPcrunch using a minimal identity of 90% for this purpose []. […]

library_books

Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen

2010
BMC Genomics
PMCID: 2846917
PMID: 20219135
DOI: 10.1186/1471-2164-11-164

[…] Tool (ACT) []. Full genome sequence comparisons were performed using the BLAST program bl2seq. Comparisons were done at protein level with an e-value cut-off of 1E-08. Blast results were parsed with MSPcrunch and the resulting files visualized with ACT. In order to improve the visualization of synteny in the graphical alignments, the start regions of the H. pylori and H. hepaticus genome sequence […]

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