ms-intersect(1)

NAME

ms-intersect - Report genes common to some species and missing from others

SYNOPSIS

ms-intersect file.gff3 file.gff3 [--diverged file.gff3 file.gff3]

OPTIONS

--diverged
    Begin list of diverged species, each of which is individually compared to the intersection of the initial group.

DESCRIPTION
ms-intersect finds the intersection of gene groups in a list of GFF3 files such as those output by ms-extract(1). I.e., it produces a list of genes neighboring a gene of interest (GOI) common to 2 or more species. This is useful since neighboring genes often contain regulatory elements for the GOI in their introns. Each GFF3 file should contain a small group of genes surrounding a gene of interest (GOI) for a given species. The filename of the GFF3 must be of the form species-gene-chrom-start.gff3 where gene is the gene name (not ID), chrom is the chromosome name or number, and start is the starting position of the gene on the chromosome. This is the filename format produced by ms-extract(1). Starting with the second GFF3 file, the intersection of genes in the file will all previous gene groups is output. Hence, the order in which files are given on the command line determines the progression of intersection output, though the final intersection of all species will be the same regardless of order, since it represents a list of genes shared by all species. If the --diverged flag is present, each GFF3 file after it is compared independently to the intersection of all groups before --diverged. This allows the user to see what genes are present in the neighboris shared by each of the diverged species

EXAMPLE
The following command shows that 3 fish species all have rbm27, rad50, and drd1b near the pou4f3 gene, while the mammals are missing rad50 and drd1b. The absence of the latter two genes may explain differences in gene regulation between fish and mammals, since they could contain regulator elements (e.g. enhancers) for pou4f3 in their introns.
ms-intersect \
    Danio_rerio-pou4f3-9-54290896.gff3 \
    Oryzias_latipes-pou4f3-14-7315063.gff3 \
    Takifugu_rubripes-pou4f3-15-5176582.gff3 \
    --diverged \
    Homo_sapiens-pou4f3-5-146338839.gff3 \
    Mus_musculus-pou4f3-18-42527604.gff3 \
    Rattus_norvegicus-pou4f3-18-34390205.gff3
====================
pou4f3
====================
Neighboring genes conserved among the original group:
Species              Ne Co Ch  Intersection with all previous genes
Danio_rerio           8  *  9  (NA)
Oryzias_latipes       8  3 14  rbm27 rad50 drd1b
Takifugu_rubripes     8  3 15  rbm27 rad50 drd1b
Genes conserved in each species through divergence from the group above:
Mus_musculus          8  1 18  rbm27
Rattus_norvegicus     8  1 18  rbm27
Homo_sapiens          8  1  5  rbm27

SEE ALSO
ms-extract(1), ms-stack(1), ms-plot(1)

BUGS
Please report bugs to the author and send patches in unified diff format. (man diff for more information)

AUTHOR
J. Bacon