Tool/Algorithm To Find Orientation Of Genes Pairs For The Set Of Genes

Question

[Ss]

Hello!

I was searching for some tool or some particular data set that can help me to download gene pairs along with their orientations and distances between them. for example

Column1 Column2 Column3 Column4
Gene1 Gene2 orientation distance_between_two

or some algorithm to do so. I have set of genes and their orientations, like

Gene1 orientation
Gene2 Orientation
Gene3 Orientation

and so on.

I kind of need an adjacency matrix for orientations of the genes in the datasets. Any ideas?

Thanks!

Answer 1

[Pierre Lindenbaum]

This question on previously asked on biostar may help you: How Can I Extract All Bidirectional Promoters In The Human Genome From Ucsc Genome Browser?

Or you could use a shell script to loop over each pair of genes:

while read L1
 do
    while read L2
      do
        echo $L1 $L2  #### DO SOME FILTERING HERE (same chromosome, etc..), e.g. USING `awk`
      done < mygenes.txt
 done  < mygenes.txt

Answer 2

[Ss]

Thanks for the reply.

I was earlier just extracting gene_name, chr_strand, start(bp), end(bp) and other details using.

   > mysql --user=anonymous 
    > --host=ensembldb.ensembl.org --database=ensembl_compara_59 --port=5306 
    > 
    > 
    > 
    > SELECT stable_id, family_id,
    > display_label, taxon_id, chr_name,
    > chr_strand, chr_start, chr_end FROM
    > member, family_member WHERE
    > member.member_id =
    > family_member.member_id AND
    > source_name = 'ENSEMBLGENE' AND
    > taxon_id = 9606 INTO OUTFILE
    > '/Datasets/family_ids.txt'

The link that you helped me with is bit difficult for me to understand as I new to MySql. I didn't follow how K1.name and K2.name can be extracted for genes.

I want to do something very similar to the example but just with genes and their orientation. thanks.

[User 59]

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