All Protein Coding Genes Of Drosophila Melanogaster

Question

[Anuraj Nayarisseri]

Hi All, I would like to download all the protein coding genes from Drosophila melanogaster either from Genbank or any other database. How to get all genes in a single file in FASTA or in .txt format.

Answer 1

[Casey Bergman]

From Flybase, select one of the following links as appropriate for your task:

• ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/fasta/dmel-all-CDS-r5.39.fasta.gz
• ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/fasta/dmel-all-transcript-r5.39.fasta.gz
• ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/fasta/dmel-all-translation-r5.39.fasta.gz
• ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.39_FB2011_07/fasta/dmel-all-gene-r5.39.fasta.gz

[Casey Bergman]

Not sure why this was down-voted. The question asks for "protein coding genes" but does not specify what level of gene structure is desired (e.g. peptides, transcripts, genes). Assuming that gene==protein (as is all to often done) is in general not a safe thing to do.

[Ido Tamir]

+1 from me, best

[Anuraj Nayarisseri]

Thanks Casey Bergman

Answer 2

[Ahdf-Lell-Kocks]

EnsemblGenomes ftp site: ftp://ftp.ensemblgenomes.org/pub/metazoa/current/fasta/drosophila_melanogaster/pep/Drosophila_melanogaster.BDGP5.pep.abinitio.fa.gz

ftp://ftp.ensemblgenomes.org/pub/metazoa/current/fasta/drosophila_melanogaster/pep/Drosophila_melanogaster.BDGP5.pep.all.fa.gz

Answer 3

[Mary]

I'm really liking the FlyMine interface: http://www.flymine.org/ And try the query builder to generate a custom query that suits your needs.

Edit: as per Casey's request, here's what I did with the query builder. Started with proteins, asked for melanogaster, and amino acids. You may want to add more, or constraints, or other things. But this is the basic structure. Gave me: Total rows:31904

If the real question is really for cDNA or for genomic DNA, it may take some tweaking from there.

[Casey Bergman]

@Mary, I'd like to +1 this solution, but try as I might (and I have many times) I find the FlyMine interface confusing and non-intuitive, except for the canned queries. Could you provide a more explicit answer of how to do a simple check-out operation like this using FlyMine, a la @Ido's response for BioMart below.

[Casey Bergman]

@Mary, really helpful - thanks for this. I was able to recreate this query from your screenshot and instructions. I'll give FlyMine another try in the future for similar tasks.

[Casey Bergman]

@Mary, really helpful - thanks for this. +1. I was able to recreate this query from your screenshot and instructions. I'll give FlyMine another try in the future for similar tasks.

[Mary]

Glad to help :) . There may be other ways to do it--start with gene, ask for CDS, etc. Depends on what you need, like most queries...

[Richard Smith]

FlyMine has Templates available for this kind of common query so you shouldn't need to use the QueryBuilder.

There is one to fetch all proteins for an organism: http://www.flymine.org/query/template.do?name=Organism_Protein

And I just added a new one to fetch all the CDSs: http://www.flymine.org/query/template.do?name=Gene_CDSs

From the results menu, click on export then select FASTA to get a file with all the sequences.

[Mary]

Great, thanks Richard. But often I do still like to get my hands on a query and build my own :)

[Casey Bergman]

@Richard. I've never gotten past the Templates (which are very useful) and understanding the QueryBuilder is something I've needed to do for a while, so I think @Mary's impetus to get folks using it more is a good thing.

[Boboppie]

@Mary really handy

Answer 4

[Ido Tamir]

Any database is a dangerous specification

Biomart:

1. biomart
2. martview (top right)
3. select latest ENSEMBL Genes
4. select dmel
5. Filter to your liking
6. Count to check if number makes sense
7. Attributes => Sequences => (Peptide?) | cDNA
8. Results

UCSC:

1. ucsc genome browser
2. table browser
3. clade: Insect
4. genome: D. mel
5. group: Genes & Gene predictions
6. output format sequence
7. get output