creating local database using ncbi ftp files in the clc main worker bench

Question

[samuelksm]

I want to create a local database using the ncbi database ftp files, am using clc main work bench to analyse my sequences (proteins), for some resean it does not connect to the ncbi serve to download the ncbi through the software, so i decided to download them manually from the server, i have tried to create a folder in the ncbi and make a local database but the software does not recognise the files , i think because they are already formated, so how can create a local database use the ftp files from ncbi

[Sean Davis]

Have you considered contacting CLC tech support?

[samuelksm]

yes but they are taking too long to get back to me, so i came here thinking , there could be any one who has had the same problem.

Answer 1

[bonoack]

Hi

I use CLC as a primary tool for all my bioinformatic analysis. Ever since KLAST was disabled on CLC, I have been using the BLAST+ tool taht is built in. While CLC has a BLAST database manager that only allows pre-formated databases from the http://ftp.ncbi.nlm.nih.gov/blast/db/ FTP site. The databases are vast and extensive, it takes too much time to run. I found custom databases from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/.

To answer your question about custom local databases. Because CLC uses BLAST+ program. I was able to use the BLAST+ STANDALONE to format all my local databases.

(I am using windows)

First, download BLAST+ on your machine from this site (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/) Documentation (http://www.ncbi.nlm.nih.gov/books/NBK52637/). Follow the instructions to add /db/ folder.

Second, format custom local databases. Download any database with a .gz file. Add it to your /db/ directory and run the following commands to create the database. Essentially converts them from .faa to the appropriate .pin, .nhr, .psi, etc...

For nucleotide fasta file: makeblastdb -in input_db -dbtype nucl -parse_seqids

For protein fasta file: makeblastdb -in input_db -dbtype prot -parse_seqids

Once formated, Simply restart CLC and refresh blast database manager and now you should have your local databases.

CREDIT source: ftp://ftp.hgc.jp/pub/mirror/ncbi/blast/documents/blastdb.html

[bonoack]

i hope this helps. If you have further questions let me know.

[samuelksm]

Thank you this was helpful