84 lines
3.1 KiB
Text
84 lines
3.1 KiB
Text
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IDENTIFY update 3 Feb 94
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NAME
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identify - creates a file of locus names corresponding to lines
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found by grep in a GenBank annotation file.
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SYNOPSIS
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identify grepfile indfile namefile findfile
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DESCRIPTION
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grepfile is created using the Unix grep command to search a .ano
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file created by splitgb. For example, to find all lines containing
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the word 'chlorophyll' in plant.ano, use
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grep -n -i 'chlorophyll' plant.ano > plant.grep
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In the example shown, the -n option causes each line written to
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plant.grep to be preceeded by the number of that line in plant.ano.
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(The -i option causes grep to ignore case.) Identify can use the
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indfile do determine which entry a given numbered line was found
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in, and writes the corresponding LOCUS name to namefile. In
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addition, all lines found in a given entry are re-written to
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findfile without the line numbers, and preceeded by the LOCUS name
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for that entry.
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EXAMPLES
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Suppose you wanted to obtain a list of names for all plant
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sequences which code for proteins. The task is complicated by the
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fact that many fungal sequences are included in the GenBank plant
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file. You could begin by searching plant.ano (containing all
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GenBank plant entries) for the word 'Planta':
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grep -n 'Planta' plant.ano > Planta.grep
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However, we want to eliminate all fungal sequences, as well as all
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sequences for RNAs other than mRNAs. If we create the file
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bad.str containing the keywords
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Mycophyta
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tRNA
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rRNA
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uRNA
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we can then type
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grep -n -f bad.str plant.ano > bad.grep
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bad.grep now contains all lines containing the offending keywords.
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We next use identify to find the names of the entries found by
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grep.
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identify Planta.grep plant.ind Planta.nam Planta.fnd
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identify bad.grep plant.ind bad.nam bad.fnd
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Next, we can use the Unix comm command to compare the two .nam
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files and produce an output file containing only names which are
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present in Planta.nam but not bad.nam:
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comm -23 Planta.nam bad.nam > plants.nam
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The file plants.nam now contains names of either plant cDNA or
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genomic sequences which do not code for structural RNAs.
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At this point, getloc could to create a sub-database containing
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only those entries listed in planta.nam. See documentation for
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getloc for a more detailed discussion.
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SEE ALSO
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grep, fgrep, egrep, ngrep, comm, splitgb, getloc
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AUTHOR
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Dr. Brian Fristensky
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Dept. of Plant Science
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University of Manitoba
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Winnipeg, MB Canada R3T 2N2
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Phone: 204-474-6085
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FAX: 204-261-5732
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frist@cc.umanitoba.ca
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REFERENCE
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Fristensky, B. (1993) Feature expressions: creating and manipulating
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sequence datasets. Nucleic Acids Research 21:5997-6003.
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