Peroxibase spacer GECA Instructions Documentation Article abstract

Description :

GECA is a collection of perl scripts, which align exon/intron structures and detect common introns and similarities between sequences in order to provide information about genes evolution and/or conservation.This is a Demo version and it's limited to 50 sequences analysis. In order to use it on a wider scale, please Download the full version.

Input Proteic section

Select Proteic sequences in Fasta format. Use one of the following fields:

  1. To upload a sequence from your local computer, select it here:
  2. To enter the sequence data manually, type here:
Input Genomic section

Input Genomic sequences in Fasta format. Use one of the following fields:

  1. To upload a sequence from your local computer, select it here:
  2. To enter the sequence data manually, type here:
Input Structure section

Input Gene Structure. Use one of the following fields :

  1. Select input type:
    GenBank format       GFF3 format
    To upload a sequence from your local computer, select it here: [?]
  2. To enter the sequence data manually, type here: [?]

CIWOG program
Common Introns Within Orthologous Genes (2009 Wilkerson MD & al. CIWOG) seeks common introns in groups of orthologous genes or families of paralogous genes.
Common introns are detected from their position and sequence conservation in the corresponding protein alignments.
The result of the research depends on the availability of genomic data and gene structures.

Parameters :

simRegion:  
minSim:      
minAbsent:  
maxSlide:    
maxGap:     

For more Informations about the input format for the different files please click here or try an example.


The Substitution Matrix

The substitution matrix by default is BLOSUM62. To use another matrix, please select from the following :


Options for MAFFT: Output order =       maxiterate:      Gap Opening Penalty:      Gap Extention Penalty     




CITATIONS

For publication of results, please cite:

GECA: a fast tool for Gene Evolution and Conservation Analysis in eukaryotic protein families.
FAWAL N & al., Bioinformatics (2012) 28 (10): 1398-1399.

View the abstract.


PORTABLE VERSION

Would you prefer to run GECA at your own site? GECA software package is available and includes links to MAFFT (Kazutaka et al., 2002) and CIWOG (Wilkerson et al., 2009). to Download, click here.



GETTING HELP

For questions, please contact : Peroxibase@lrsv.ups-tlse.fr




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