FrameDP protocols

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description
FrameDP computational protocol

FrameDP specifications

Information


Unique identifier OMICS_14664
Name FrameDP
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Version 1.2.2
Stability Stable
Maintained Yes

Maintainer


  • person_outline Thomas Schiex <>

Information


Unique identifier OMICS_14664
Name FrameDP
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Thomas Schiex <>

Publication for FrameDP

FrameDP IN pipelines

 (3)
2016
PMCID: 5150578
PMID: 27941947
DOI: 10.1038/srep39007

[…] assessed through blastx searches against swissprot (e-value ≤ 1e–6) and the corresponding amino acid sequences translated using an in-house script. the contigs without translation were submitted to framedp software41 and the remaining contigs were analysed with estscan42. transcripts resulting from these two last sequence identification steps were searched using blastp against the non-redundant […]

2014
PMCID: 4268816
PMID: 25440955
DOI: 10.1186/s13071-014-0527-1

[…] database of kyoto encyclopedia of genes and genomes (kegg). among the annotated unigenes, 61,941 coding sequences (cds) were obtained by the blastx algorithm [24]. all cdss were analyzed using the framedp software [25], which has the ability to self-train directly on est clusters instead of requiring curated cdna sets to train the underlying estscan and decoder software [26]., to minimise […]

2012
PMCID: 3319000
PMID: 22215803
DOI: 10.1093/gbe/evr140

[…] transcripts were then compared with predicted a. pisum proteins trough blastx (altschul et al. 1990). this information helped to identify potential homology and was used for cds reconstruction with framedp, a pipeline developed at the inra of toulouse (schiex et al. 2003)., to annotate the five new est gene sets (and also all the a. pisum genes), we used blast2go (conesa et al. 2005) […]

FrameDP institution(s)
Laboratoire Interactions Plantes Micro-organismes (LIPM) UMR441/2594, INRA/CNRS, Castanet Tolosan, France; Unité de Biométrie et d’Intelligence Artificielle UR 875, INRA, Castanet Tolosan, France

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