How To Get A List Of All Human Genes Above A Certain Length

Question

[Whetting]

Hi,

I want to assemble a list of human genes longer than a specified length. Any ideas on how to accomplish such a feat?

Thanks!

Answer 1

[Ashutosh Pandey]

Try this command :

$ mysql --user=genome -N --host=genome-mysql.cse.ucsc.edu -A -D hg19  -e "select name,name2,txEnd - txStart from refGene"  > Gene_sizes.txt

You can sort Gene_sizes file now using length that is in the third column. The table includes all the Refseq transcripts for a gene. You can get multiple information from UCSC. See the table schema: http://genome.ucsc.edu/cgi-bin/hgTables

[Rm]

I was about to paste this: to limit above 1000 bases and dispaly top 20:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e ' select distinct name, chrom, txStart, txEnd, (txEnd - txStart) as length from refGene where (txEnd - txStart) > 1000 limit 20'

[Steve Lianoglou]

I'm curious if the OP wants this length (from transcription start to end) or the eventual length of the transcript generated (ie. the length after introns have been spliced out).

[Rm]

Question was not specific: there are few ways to get the information: start to end; sum all the exon length in a transcript etc.

[cdsouthan]

Simplest just to sort Swiss-Prot Human by protein size ?