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

SeqTools article

SeqTools citations

 (3)
2017
PMCID: 5509035

[…] 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 […]

2014
PMCID: 3963999

[…] genes that passed the 95% confidence level in 3 or 4 of the arrays were considered to demonstrate differential expression. these genes were then clustered on the basis of their sequence, using seqtools (http://www.seqtool.dk) to identify unique sequences. gene ontology (go) functions were assigned using blast2go (http://www.blast2go) based on blastx homologies., the 5k microarray was used […]

2008
PMCID: 2478663

[…] 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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