NCBI FASTA files are a bit crazy
1
0
Entering edit mode
9.4 years ago
flame233 ▴ 10

Hello everyone. I am new to bioinformatics, although I have been around these forums for a while.

As for my question, I am working with protein sequences from completed genomes of a bacteria, but I have noticed that something weird (or interesting) happens to the downloaded proteomes and genomes that I download from the NCBI site.

After the downloads are completed, for [Ref_Seq] sequences, two things happen: either an error message appear at the end of the sequence as "Resource temporarily unavailable (4).", or every file I download has a different amount of lines, gene amounts and data size.

Is this normal?. Maybe is not statistically significant in the analysis? Is there any way to improve this?

Thank you. And apologies for my grammar

FASTA Proteome NCBI Genome • 2.3k views
ADD COMMENT
0
Entering edit mode

How are you downloading this data and from what location?

ADD REPLY
0
Entering edit mode

From: http://www.ncbi.nlm.nih.gov/nuccore/NC_017534.1

Send tab -> Coding sequences -> FASTA Protein

ADD REPLY
0
Entering edit mode

Probably it's because of your internet connection or something like that: it either cannot connect or breaks in the middle (therefore different number of lines). If you are downloading something important use ftp, don't rely on their website tool.

ADD REPLY
0
Entering edit mode

Yes, FTP worked perfectly, thanks everyone for your help

ADD REPLY
1
Entering edit mode
9.4 years ago
GenoMax 147k

I suggest that you download the .fna and .faa (DNA and Protein) files directly from respective genome folders in: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/

That said I have not had any problems downloading sequences using the method you mentioned above.

ADD COMMENT
0
Entering edit mode

Thanks, I will give it a try and post feedback :)

Edit: It worked perfectly, I can access the whole sequence with no trouble. Thanks a lot :)

ADD REPLY

Login before adding your answer.

Traffic: 2564 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6