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>EXTRACT</TITLE
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>EXTRACT</H1
><DIV
CLASS="REFNAMEDIV"
><A
NAME="AEN15"
></A
><H2
>Name</H2
>extract -- Fine start/stop positions of genes in genome sequence</DIV
><DIV
CLASS="REFSYNOPSISDIV"
><A
NAME="AEN18"
></A
><H2
>Synopsis</H2
><P
><B
CLASS="COMMAND"
>long-orgs</B
> [genome-file <VAR
CLASS="OPTION"
><VAR
CLASS="REPLACEABLE"
>options</VAR
></VAR
>]</P
></DIV
><DIV
CLASS="REFSECT1"
><A
NAME="AEN24"
></A
><H2
>DESCRIPTION</H2
><P
>Program extract takes a FASTA format sequence file and a file
with a list of start/stop positions in that file (e.g., as produced
by the long-orfs program) and extracts and outputs the
specified sequences.</P
><P
>The first command-line argument is the name of the sequence file,
which must be in FASTA format.</P
><P
>The second command-line argument is the name of the coordinate file.
It must contain a list of pairs of positions in the first file, one
per line. The format of each entry is:</P
><P
> <IDstring>> <start position> <stop position></P
><P
>This file should contain no other information, so if you're using
the output of glimmer or long-orfs , you'll have to cut off
header lines.</P
><P
>The output of the program goes to the standard output and has one
line for each line in the coordinate file. Each line contains
the IDstring , followed by white space, followed by the substring
of the sequence file specified by the coordinate pair. Specifically,
the substring starts at the first position of the pair and ends at
the second position (inclusive). If the first position is bigger
than the second, then the DNA reverse complement of each position
is generated. Start/stop pairs that "wrap around" the end of the
genome are allowed.</P
></DIV
><DIV
CLASS="REFSECT1"
><A
NAME="AEN32"
></A
><H2
>OPTIONS</H2
><P
></P
><DIV
CLASS="VARIABLELIST"
><DL
><DT
><VAR
CLASS="OPTION"
>-skip</VAR
></DT
><DD
><P
> makes the output omit the first 3 characters of each sequence, i.e., it skips over the start codon. This was the behaviour of the previous version of the program.</P
></DD
><DT
><VAR
CLASS="OPTION"
>-l</VAR
></DT
><DD
><P
> makes the output omit an sequences shorter than n characters.
n includes the 3 skipped characters if the -skip switch
is one.
</P
></DD
></DL
></DIV
></DIV
><DIV
CLASS="REFSECT1"
><A
NAME="AEN45"
></A
><H2
>SEE ALSO</H2
><P
>glimmer2 (1),
long-orfs (1),
adjust (1),
anomaly (1),
build-icm (1),
check (1),
codon-usage (1),
compare-lists (1),
extract (1),
generate (1),
get-len (1),
get-putative (1),</P
><P
>http://www.tigr.org/software/glimmer/</P
><P
>Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer2.</P
></DIV
><DIV
CLASS="REFSECT1"
><A
NAME="AEN50"
></A
><H2
>AUTHOR</H2
><P
>This manual page was quickly copied from the glimmer web site by Steffen Moeller <CODE
CLASS="EMAIL"
><<A
HREF="mailto:moeller@pzr.uni-rostock.de"
>moeller@pzr.uni-rostock.de</A
>></CODE
> for
the <SPAN
CLASS="PRODUCTNAME"
>Debian</SPAN
> system.
</P
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