Question: Are old versions of NCBI's nt stored somewhere?
0
gravatar for felix.kuo.1211
2.3 years ago by
felix.kuo.121110 wrote:

I have learn something, so I change my question

I have know that NCBI has stopped supporting gi numbers. It change to use Accessions.

So I have to find a gi fromat nt for use.

Is there any way to download?

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by felix.kuo.121110
1

See my answer in the following post:

where can I get environmental bacteria genome in fasta format (as many as possible)?

It will help you to find a previous NCBI bacterial-version as well as a current one.

I've looked into some random bacterial genome from old NCBI-verion, there are gi-numbers here.

See the link below:

ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_refseq/Bacteria/Acholeplasma_palmae_J233_uid222824/NC_022538.faa

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by natasha.sernova3.1k

I see, thanks. But it is not non-redundant, right?

ADD REPLYlink written 2.3 years ago by felix.kuo.121110

It's simply some old version of a previous version of NCBI database.

It's a good idea to ask NCBI-people about redundancy.

Or read README-files carefully, they created a lot of such files to explain all the details of this transition to a new version.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by natasha.sernova3.1k

The directory linked by @Natasha is just an old version (appears to be from 2013) of the RefSeq bacterial genomes (the direct link is only for one bacterium Acholaeplasma oalmae). There also you would need to download the .faa files from each of the directories listed to make up your starting "bacterial genomes" file.

ADD REPLYlink written 2.3 years ago by genomax59k

If you have accession numbers you can use this technique: A: NCBI Blast locally: filter by accession number and NOT by GI number

Blast db indexes being large you are going to be hard-pressed to find an older version. Can I ask what exactly you are trying to do that you must have a subset of bacteria? Can you not filter the results afterwards?

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by genomax59k

I try to download accesion list from NCBI but it's to slow...12Hr 60MB. idon't know why? I want to make a bacteria NT subset, or download a whole non-redundant bacteria genome forgi formate.

I want to use mapping some file. And find all the bacteria(not only 16s).

Can you give me some tips?

ADD REPLYlink written 2.3 years ago by felix.kuo.121110

You are still not describing what it is you want to do after you extract those bacterial genomes. Perhaps we can devise an alternate solution.

ADD REPLYlink written 2.3 years ago by genomax59k

Oh I see

Simple=bowtie2(whole bactireia)=filter=>bactireial Simple

bactireial Simple =bowtie2(Silva rRNA DB) =>rRNA Reads=>Taxonomy Assignment

bactireial Simple =bowtie2(Silva rRNA DB) =>Putative mRNA Reads=>Functional Annotation

Putative mRNA Reads=RSEM=>Gene Expression Analysis=KEGG=>Metabolic

Putative mRNA Reads=BLASTx(COG)=>Functional Categories Analysis

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by felix.kuo.121110

It would be much simpler to use MEGAN6.

ADD REPLYlink written 2.3 years ago by genomax59k
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