Approaches to Web Development for Bioinformatics

Medical Computing > Web Development for Bioinformatics > Public Databases > NCBI > Human Genome
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Human Genome

The human genome is given in a number of different files and formats. The messenger RNA (mRNA) is given in a file called rna.gbk.gz. This includes each locus with reference identifiers, PubMed references, mRNA, a comment, and the gene product (usually a protein).  Here are a few sample lines


GenBank mRNA file fragment

LOCUS       NM_004239               6452 bp    mRNA    linear   PRI 16-OCT-2005
DEFINITION  Homo sapiens thyroid hormone receptor interactor 11 (TRIP11), mRNA.
...
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from Y12490.1.
           
            Summary: TRIP11 was first identified through its ability to
            interact functionally with thyroid hormone receptor-beta (THRB; MIM
            190160). It has also been found in association with the Golgi
            apparatus and microtubules.[supplied by OMIM].
FEATURES             Location/Qualifiers
...
                    /db_xref="GeneID:9321"

A program that scans this file and extracts the gene ID, locus accession reference, and comment to another file is given below.


Perl

#!/usr/bin/perl -w
# A Perl script to extract comments on gene locii from the file rna.gbk
# The number of locii read
my $i = 0;

# The locus accession reference
my $accession;

# The text for the comment
my $comment;

# The RNA file must be in GenBank form and be called rna.gbk
open RNA_GBK, "<", "rna.gbk";

# The output file
open COMMENTS_RNA, ">", "comments_rna.gbk";

# Iterate over each line in the input file
while (<RNA_GBK>) {

# Look for the start of a new comment in a line beginning with 'LOCUS'
if ($_ =~ /^(LOCUS)(\s+)([A-Z0-9_]+)/) {
$accession = $3;
$i++;

# Look for a comment
} elsif ($_ =~ /^(COMMENT)(\s+)(.*)/) {
$comment = $3;
# Concatenate subsequent comment lines
while (<RNA_GBK>) {
if ($_ =~ /^(\s+)(.*)/) {
$comment .= " $2";
} else {
last;
}
}
}

# Look for the NCBI gene ID.  This is found within the features block
if ($_ =~ /^FEATURES/) {
my $geneID;
while (<RNA_GBK>) {
if ($_ =~ /(GeneID:)([0-9]+)/) {
$geneID .= $2;
print(COMMENTS_RNA "$geneID\t$accession\t$comment\n");
last;
}
}
}
}
print "$i Locii written.\n";

close RNA_GBK;
close COMMENTS_RNA;

The comment can then be more easily searched and extracted with a simple script, such as


Perl

#!/usr/bin/perl -w
# A Perl script to greg comments from the file comments_rna.gbk, extracted from the file rna.gbk
open COMMENTS_RNA, "<", "comments_rna.gbk";

# gene ID 9321 is an example
my @line = grep {/^9321/} <COMMENTS_RNA>;
my @fields = split /\t/, $line[0];
print $fields[2];
close COMMENTS_RNA;

This is used in conjuntion with the scripts above to produce the detailed comments for the human gene search page on this site.


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