Retrieve One Coding Sequences For Each Gene

Question

[Mohammad Reza Bakhtiarizadeh]

Dear all I want to retrieve all of coding sequences (CDS) related to a special organism (for example, human) but i don't want to have several coding sequences for each gene. in other words i want to have one CDS for each gene (canonical transcript of each protein-coding gene). i tried Biomart but it cant do it. if there is any way to fix my problem please inform me. i really need your help. thanks a lot in advance best regards

Answer 1

[Leszek]

Usually people use the longest isoform. So get all transcripts from given species and keep only the longest for each gene.

[Mohammad Reza Bakhtiarizadeh]

Dear Leszek Thanks for your help. but i am not familiar with Perl or language programming like this as well. if possible help me more about this. thanks again for your help regards

[Nisa]

dear Leszek, i wanna ask u bout neighbour-joining tree (PHYLIP version) .. my OUTGROUP that i choose to be the root were always in INGROUP. why these happened? n wat should i do to get the outgroup for the tree?

Answer 2

[Bioinfosm]

You can download the refFlat file from UCSC and use the exon coordinates to sum them up to a coding length. As @Leszek mentioned, a common way is to take a union of all exons for a gene and generate 'the longest isoform'. Some scripting would be needed to generate such a file.

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ -> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz