ReLA specifications

Information


Unique identifier OMICS_10966
Name ReLA
Alternative name REgulatory region Local Alignment tool
Interface Web user interface
Restrictions to use None
Input data Reference sequence, sequences to compare with the reference sequence, TFBSs position frequency matrices
Input format FASTA
Output data ReLA generates a graph showing the distribution of all accepted preliminary predictions on the reference sequence. From the analysis of the overlap among these preliminary predictions, we generate the final prediction by selecting the region, between 200 and 1000 nt long that contains the highest number of preliminary candidate predictions. Together with the final prediction on the reference sequence, additional consensus regions are also defined in each of the other sequences, which correspond to those (if any) that match the final predicted promoter region. We also provide the list of all conserved TFBSs. From this list, a subset of the most conserved TFBSs (specifically, those within the top 10% of conservation) is selected and used to generate a multiple alignment in graphical format.
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_10966
Name ReLA
Alternative name REgulatory region Local Alignment tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data Reference sequence, sequences to compare with the reference sequence, TFBSs position frequency matrices
Input format FASTA
Output data ReLA generates a graph showing the distribution of all accepted preliminary predictions on the reference sequence. From the analysis of the overlap among these preliminary predictions, we generate the final prediction by selecting the region, between 200 and 1000 nt long that contains the highest number of preliminary candidate predictions. Together with the final prediction on the reference sequence, additional consensus regions are also defined in each of the other sequences, which correspond to those (if any) that match the final predicted promoter region. We also provide the list of all conserved TFBSs. From this list, a subset of the most conserved TFBSs (specifically, those within the top 10% of conservation) is selected and used to generate a multiple alignment in graphical format.
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publication for REgulatory region Local Alignment tool

ReLA institution(s)
Joint IRB-BSC program on Computational Biology, BSC c/ Jordi Girona, Barcelona, Spain
ReLA funding source(s)
Ministerio EspaƱol de Ciencia e InnovaciĆ³n (BIO2006-15036)

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