ReLA specifications

Unique identifier:
OMICS_10966
Interface:
Web user interface
Input data:
Reference sequence, sequences to compare with the reference sequence, TFBSs position frequency matrices
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.
Stability:
Stable
Name:
REgulatory region Local Alignment tool
Restrictions to use:
None
Input format:
FASTA
Computer skills:
Basic
Maintained:
Yes

ReLA specifications

Unique identifier:
OMICS_10966
Software type:
Application/Script
Restrictions to use:
None
Input format:
FASTA
Operating system:
Unix/Linux
Stability:
Stable
Name:
REgulatory region Local Alignment tool
Interface:
Command line interface
Input data:
Reference sequence, sequences to compare with the reference sequence, TFBSs position frequency matrices
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:
Advanced
Maintained:
Yes

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ReLA distribution

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ReLA support

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Publications

Institution(s)

Joint IRB-BSC program on Computational Biology, BSC c/ Jordi Girona, Barcelona, Spain

Funding source(s)

Ministerio Español de Ciencia e Innovación (BIO2006-15036)

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