Package Bio :: Package AlignAce :: Module AlignAceStandalone
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Module AlignAceStandalone

source code

This module provides code to work with the standalone version of AlignACE, for motif search in DNA sequences.

AlignACE homepage:

http://atlas.med.harvard.edu/

AlignACE Citations:

Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae, Hughes, JD, Estep, PW, Tavazoie S, & GM Church, Journal of Molecular Biology 2000 Mar 10;296(5):1205-14.

Finding DNA Regulatory Motifs within Unaligned Non-Coding Sequences Clustered by Whole-Genome mRNA Quantitation, Roth, FR, Hughes, JD, Estep, PE & GM Church, Nature Biotechnology 1998 Oct;16(10):939-45.

functions: AlignAce - runs the AlignACE standalone prgram and returns the ApplicationResult object

Functions [hide private]
 
AlignAce(infile, cmd='AlignACE', **keywds)
Runs AlignACE and returns data.
source code
Variables [hide private]
  __package__ = 'Bio.AlignAce'
Function Details [hide private]

AlignAce(infile, cmd='AlignACE', **keywds)

source code 

Runs AlignACE and returns data.

cmd == AlignACE executable infile == sequence file to process

You may pass more parameters to **keywds to change the behavior of the search. Otherwise, optional values will be chosen by blastall.

numcols number of columns to align (10) expect number of sites expected in model (10) gcback background fractional GC content of input sequence (0.38) minpass minimum number of non-improved passes in phase 1 (200) seed set seed for random number generator (time) undersample possible sites / (expect * numcols * seedings) (1) oversample 1/undersample (1)