gfServer

Reference Code backup Executable files

Make a server to quickly find where DNA occurs in genome. To set up a server:gfServer start host port file(s)Where the files are .nib or .2bit format files specified relative to the current directory.To remove a server:gfServer stop host portTo query a server with DNA sequence:gfServer query host port probe.faTo query a server with protein sequence:gfServer protQuery host port probe.faTo query a server with translated dna sequence:gfServer transQuery host port probe.faTo query server with PCR primersgfServer pcr host port fPrimer rPrimer maxDistanceTo process one probe fa file against a .nib format genome (not starting server):gfServer direct probe.fa file(s).nibTo test pcr without starting server:gfServer pcrDirect fPrimer rPrimer file(s).nib

Category

Mapping

Usage

gfServer status host port

Manual

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

To get input file list
gfServer files host port
Options:
-tileSize=N size of n-mers to index. Default is 11 for nucleotides, 4 for
proteins (or translated nucleotides).
-stepSize=N spacing between tiles. Default is tileSize.
-minMatch=N Number of n-mer matches that trigger detailed alignment
Default is 2 for nucleotides, 3 for protiens.
-maxGap=NNumber of insertions or deletions allowed between n-mers.
Default is 2 for nucleotides, 0 for protiens.
-trans Translate database to protein in 6 frames. Note: it is best
to run this on RepeatMasked data in this case.
-log=logFile keep a log file that records server requests.
-seqLog Include sequences in log file (not logged with -syslog)
-ipLog Include user's IP in log file (not logged with -syslog)
-syslog Log to syslog
-logFacility=facility log to the specified syslog facility - default local0.
-maskUse masking from nib file.
-repMatch=N Number of occurrences of a tile (nmer) that trigger repeat masking the tile.
Default is 1024.
-maxDnaHits=N Maximum number of hits for a dna query that are sent from the server.
Default is 100.
-maxTransHits=N Maximum number of hits for a translated query that are sent from the server.
Default is 200.
-maxNtSize=N Maximum size of untranslated DNA query sequence
Default is 40000
-maxAaSize=N Maximum size of protein or translated DNA queries
Default is 8000
-canStop If set then a quit message will actually take down the
server

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