Promoter Sequences For Non Model Organism From Old Gene Build

Question

[Sudeep]

Hi All,
I have a set of genes (Entrez gene ids) for which I need promoter sequences. Now my genes are from a non model organism (Sus scrofa or pig) using an earlier gene build (Sscrofa9.2 build). I have seen Yuri's post and answers on retrieving promoter sequences and I like the idea of retrieving sequences from Ensembl Biomart. But my concerns are
1. what about genes that cannot be mapped to Ensembl and
2. If a gene (Entrez gene id) has more than one mapping Ensembl gene id which one should I take ?
Now what I plan to do is
1. retrieve genbank and fasta files from NCBI genome ftp
2. parse genbank files for gene co - ordinates and finally
3. parse chromosome fasta file for 1,000 bp region upstream of gene start position.
But before that does anybody have a much more easier suggestion ? and if I parse the genbank and fasta files, is it possible to get sense - antisense strand information ? and what about the length of upstream sequence that I should take ?

Thank you in advance.

Answer 1

[14134125465346445]

Ensembl applies a series of rules to do the mapping between different gene sets from different assemblies or gene predictions. In Biomart, you can choose "Filters" and give the list of "Protein (Genbank) ID(s)" [e.g. BAA20017] for which you want the sequences and then in Attributes choose "Flank (Gene) Upstream flank [1000]".

http://www.ensembl.org/Help/Faq?id=125