NCBI FASTA files are a bit crazy

Question

[flame233]

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

[GenoMax]

How are you downloading this data and from what location?

[flame233]

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

Send tab -> Coding sequences -> FASTA Protein

[marina.v.yurieva]

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.

[flame233]

Yes, FTP worked perfectly, thanks everyone for your help

Answer 1

[GenoMax]

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.

[flame233]

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 :)