SeqTools protocols

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description
SeqTools computational protocol

SeqTools specifications

Information


Unique identifier OMICS_23182
Name SeqTools
Software type Application/Script, Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Input format GFF3/FASTA,FASTA+FASTA, STOCKHOLM,MSF,SELEX,FASTA
Output format STOCKHOLM,MSF,SELEX,FASTA,PDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License GNU General Public License version 3.0
Computer skills Medium
Version 4.37.0
Stability Stable
Requirements
GTK
Maintained Yes

Subtool


  • Blixem

Versioning


Add your version

Maintainer


  • person_outline Gemma Barson <>

Additional information


ftp://ftp.sanger.ac.uk/pub/resources/software/seqtools/Docs/User_doc/index.html

Publication for SeqTools

SeqTools IN pipelines

 (5)
2017
PMCID: 5509035
PMID: 28854627
DOI: 10.1093/gbe/evx114

[…] the neanderthal (http://cdna.eva.mpg.de/neandertal/altai/altaineandertal/vcf) and denisovan (http://cdna.eva.mpg.de/denisova/vcf/hg19_1000g/) data sets, using a custom tool called vcf2fasta in the seqtools_v2.2 package (https://github.com/jsharbrough/seqtools). variants were filtered based on basecall quality (≥q30) and depth (≥10×). we mapped n-mt refseq genes to the huref alternate genome […]

2016
PMCID: 5104789
PMID: 27942245
DOI: 10.1007/s11032-016-0569-5

[…] v7.1.11 (hall 1999). the identification of nucleic and amino acid sequences present in more than one copy, as well as the elaboration of clusters grouping identical sequences, were carried out with seqtools v8.4.042 (http://www.seqtools.dk/). this software was also used to search for homologies with all α-gliadin proteins in genbank via a blastp analysis (date of analysis: 23 october 2015)., […]

2016
PMCID: 5104789
PMID: 27942245
DOI: 10.1007/s11032-016-0569-5

[…] of nucleic and amino acid sequences present in more than one copy, as well as the elaboration of clusters grouping identical sequences, were carried out with seqtools v8.4.042 (http://www.seqtools.dk/). this software was also used to search for homologies with all α-gliadin proteins in genbank via a blastp analysis (date of analysis: 23 october 2015)., the amino acid sequences […]

2008
PMCID: 2478663
PMID: 18590528
DOI: 10.1186/1471-2229-8-73

[…] using t7 primer. these sequences have been deposited in genbank under the accession numbers ex568682 to ex571416., sequence data were trimmed off vector, adaptor and low quality sequences using seqtools [50]. trimmed sequences that were shorter than 100 basepairs were excluded from further analysis. blast score-based clustering method with a score cut-off of 0.6 from seqtools was then used […]

2008
PMCID: 2478663
PMID: 18590528
DOI: 10.1186/1471-2229-8-73

[…] sequences using seqtools [50]. trimmed sequences that were shorter than 100 basepairs were excluded from further analysis. blast score-based clustering method with a score cut-off of 0.6 from seqtools was then used to assemble the sequences. all clusters and singletons resulting from this automated clustering were considered to be the best estimation of a minimal gene set for our est […]

SeqTools institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
SeqTools funding source(s)
Supported by the Wellcome Trust Grant (098051); and the National Human Genome Research Institute Grant (5U54HG00455-04).

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