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
|
StringTypes = ( <type 'str'>, <type 'unicode'>)
|
|
__package__ = ' Bio.AlignAce '
|
|
xml_support = 1
|
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)
|