Sheep Genome and Chromosome

Question

[hosin]

I have some coordinates from sheep chromosomes like : chr24:40902129-41709809 chr25:11035146-11097889 chr26:10400726-10968027 , How I can find genes in this coordinates by the fastest and newest db and methods . Please help me .Thanks.

Answer 1

[GenoMax]

Use Ensembl BioMart.

Ensembl Genes --> Sheep Gene v.3.1(hope you have the latest build) --> Filters (left column) --> Multiple Regions --> Paste in your intervals (500 at one time max, remove prefix chr from intervals) --> Attributes (left column) --> Gene --> select Gene Name --> Click on count(top left of page) --> Results.

[hosin]

Thank you. But unfortunatly I have V4.0 version

Answer 2

[WouterDeCoster]

Download a bed file from the UCSC table browser and use bedtools

Answer 3

[Pierre Lindenbaum]

using mysql/ucsc

$ echo -e "chr19:50686000-50700183\nchr24:40902129-41709809\nchr25:11035146-11097889" |\
  awk -F '[:-]' 'BEGIN{printf("select * from refGene where ");} {printf("%s (chrom=\"%s\" and NOT(txEnd<%d OR txStart>%d)) ",(NR==1?"":" OR "),$1,$2,$3);} END {printf(";\n");}'  | \
 mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 -D oviAri3  -t
+-----+--------------+-------+--------+----------+----------+----------+----------+-----------+--------------------------------------+--------------------------------------+-------+-------+--------------+------------+------------+
| bin | name         | chrom | strand | txStart  | txEnd    | cdsStart | cdsEnd   | exonCount | exonStarts                           | exonEnds                             | score | name2 | cdsStartStat | cdsEndStat | exonFrames |
+-----+--------------+-------+--------+----------+----------+----------+----------+-----------+--------------------------------------+--------------------------------------+-------+-------+--------------+------------+------------+
| 971 | NM_001161875 | chr19 | +      | 50686975 | 50696070 | 50686975 | 50696070 |         4 | 50686975,50691449,50695264,50695896, | 50687131,50691570,50695395,50696070, |     0 | RHOA  | cmpl         | cmpl       | 0,0,1,0,   |
+-----+--------------+-------+--------+----------+----------+----------+----------+-----------+--------------------------------------+--------------------------------------+-------+-------+--------------+------------+------------+