Finding out Cytobands/Idiograms for assemblies

Fri, 05 Oct 2012 16:01:58 -0700
biology, genetics, snp, tech

In many organisms it is common to use idiograms or cytobands which provide information on approximately where something is located on a chromosome in reference to the chromosome's larger structure, or when exact locations are not required.

Until recently, I didn't know where NCBI kept their idiogram annotations, which made my mirror of dbsnp (which I use to annotate my whole genome analyses) slightly less useful than it could have been. But, after a bit of searching of NCBI's ftp site, I was able to locate the file in the new movie directory: ideogram_9606_GCF_000001305.13_850_V1.

Then, a quick bit of work with SQL, I have the following schema:

CREATE TABLE idiogram (
       chr TEXT NOT NULL,
       pq  TEXT NOT NULL,
       idiogram TEXT NOT NULL,
       -- I think these are related to recombination rates, but I'm not sure
       rstart INT NOT NULL,
       rstop INT NOT NULL,
       start INT NOT NULL,
       stop INT NOT NULL,
       -- I believe this indicates whether the band is black or white
       posneg TEXT NOT NULL
       );

CREATE UNIQUE INDEX ON idiogram(chr,pq,ideogram);
CREATE UNIQUE INDEX ON idiogram(chr,start);
CREATE UNIQUE INDEX ON idiogram(chr,stop);

and an additional bit of SQL in my SNP annotation perl script:

SELECT CONCAT(chr,pq,idiogram) AS idiogram
  FROM idiogram
  WHERE idiogram.chr = ? AND idiogram.start <= ? AND idiogram.stop < ? LIMIT 1;

and some code:

sub find_idiogram {
    my %param = @_;

    my %info;
    my $rv = $param{sth}->execute($param{chr},$param{pos},$param{pos}) //
    die "Unable to execute statement properly: ".$param{dbh}->errstr;
    my ($idiogram) = map {ref $_ ?@{$_}:()} map {ref $_ ?@{$_}:()} $param{sth}->fetchall_arrayref([0]);
    if ($param{sth}->err) {
    print STDERR $param{sth}->errstr;
    $param{sth}->finish;
    return 'NA';
    }
    $param{sth}->finish;
    return $idiogram // 'NA';
}

and viola:

id | chr | pos | idiogram | ref | alt | orig_id | gene | [...]
rs10000010 | 4 | 21618674 | 4p16.3 | T | C | rs10000010 | KCNIP4 | [...]

idiograms for every SNP.