Category

Generic


Usage

blastXmlToPsl [options] blastXml psl


Manual

This tool is part of UCSC Genome Browser's utilities.


options:
-scores=file - Write score information to this file. Format is:
strands qName qStart qEnd tName tStart tEnd bitscore eVal qDef tDef
-verbose=n - n >= 3 prints each line of file after parsing.
n >= 4 dumps the result of each query
-eVal=n n is e-value threshold to filter results. Format can be either
an integer, double or 1e-10. Default is no filter.
-pslx - create PSLX output (includes sequences for blocks)
-convertToNucCoords - convert protein to nucleic alignments to nucleic
to nucleic coordinates
-qName=src - define element used to obtain the qName. The following
values are support:
o query-ID - use contents of the element if it
exists, otherwise use
o query-def0 - use the first white-space separated word of the
element if it exists, otherwise the first word
of .
Default is query-def0.
-tName=src - define element used to obtain the tName. The following
values are support:
o Hit_id - use contents of the element.
o Hit_def0 - use the first white-space separated word of the
element.
o Hit_accession - contents of the element.
Default is Hit-def0.
-forcePsiBlast - treat as output of PSI-BLAST. blast-2.2.16 and maybe
others indentify psiblast as blastp.
Output only results of last round from PSI BLAST


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