Question: Tool/Algorithm To Find Orientation Of Genes Pairs For The Set Of Genes
1
gravatar for Ss
8.0 years ago by
Ss50
Ss50 wrote:

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

ans so on.

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

Thanks!

tool • 1.5k views
ADD COMMENTlink modified 8.0 years ago • written 8.0 years ago by Ss50
0
gravatar for Pierre Lindenbaum
8.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum122k wrote:

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
ADD COMMENTlink modified 3 hours ago by RamRS24k • written 8.0 years ago by Pierre Lindenbaum122k
0
gravatar for Ss
8.0 years ago by
Ss50
Ss50 wrote:

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.

ADD COMMENTlink written 8.0 years ago by Ss50

Please add this as a comment to the question, not as an answer itself in future. Answers are not meant for additional clarification. You could even go back and re-edit the question if you feel that is necessary to include more information.

ADD REPLYlink written 8.0 years ago by Daniel Swan13k
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