Tuiuiu

By | September 22, 2011

Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats.

Tuiuiu is used as a preliminary step before applying a multiple local aligner tool.

OPTIONS:
–excellent|–good : algorithm used (default is excellent)
–mono|–multi : number of sequences (default is multi)
-w value : length of the window (default 100)
-e value : number of errors (substitutions, insertions and deletions) between two windows (default 12)
-r value : number of window searched (default 8) -k value : length of the k-mers (default 6 decreasing to a good threshold)
-c : ask to check direct AND reverse complement strands
-N {0 1 2} :
2: Write Ns instead of filtered nucleotides, (default)
1: Concatenate concerved fragments, separated with one ‘N’
0: Concatenate concerved fragments

Name
Tuiuiu
Documentation
http://training.genouest.org/claroline/claroline/learnPath/learningPathList.php?cidReset=true&cidReq=TUIUIU
Protocol
SOAP
WSDL
Endpoint
http://webservices.genouest.org/opal2/services/Tuiuiu
Topic
Sequence Analysis
Type
Analysis
Tags
Description

Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain [...]

Further information

Tuiuiu removes from a sequence or from a set of sequences areas as large as possible that do not contain researched repeats.

Tuiuiu is used as a preliminary step before applying a multiple local aligner tool.

OPTIONS:
–excellent|–good : algorithm used (default is excellent)
–mono|–multi : number of sequences (default is multi)
-w value : length of the window (default 100)
-e value : number of errors (substitutions, insertions and deletions) between two windows (default 12)
-r value : number of window searched (default 8) -k value : length of the k-mers (default 6 decreasing to a good threshold)
-c : ask to check direct AND reverse complement strands
-N {0 1 2} :
2: Write Ns instead of filtered nucleotides, (default)
1: Concatenate concerved fragments, separated with one ‘N’
0: Concatenate concerved fragments

Original source
BioCatalogue

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