NCBI Blaster

NCBI BLAST automation tool

The way bioinformatics should be...

NCBI Blaster (aka BLAST Robot) is a freeware biology software tool from the Avalanche NextGen package that automates the NCBI BLAST search processes.

It automates the NCBI BLAST alignment of coding DNA or protein sequences and processes the results for visualization. The program seamlessly integrates with DNA Sequence Assembler and collects the contigs generated during manual or automatic (batch) sequence assembly, sends queries to NCBI Blast server and automatically download the results (the GBK files) to disk then it helps the user to analyze its data.

The program is in early development stage. The following modules are ready. 

How to use it

Start NCBI Blaster. Enter the DNA sequence you want to align and the alignment parameters. Enter project's output path. Press 'Start BLAST' and wait few seconds. The resulted GenBank (GBK) files are automatically downloaded from NCBI server and stored in project's folder.

Supported files

NCBI Blaster utility only support Fasta/SEQ files. Support for SFF, FastQ, SCF, ABI is already under way.

Download

Requirements

• < 3MB of disk space
• < 30MB free RAM
• No Java, no .Net
• Windows XP and up
• No installation required

Portability

This software tool is really small so you can easily copy it on a floppy disk or USB flash stick and take it with you or send it to your colleagues via email.

The EUtils module

EUtils is one of the modules in Blast Robot. It works with the Entrez databases at NCBI. NCBI provides EUtils as a web service but our module can query Entrez directly, rather than going through the web interface and dealing with the hassles of web scraping. These greatly simplify working with the Entrez databases.

Example: We can use this module to get all protein sequences related to protein GI:4579714:

>gi|27450749|gb|AAO14677.1|AF508258_1 rhodopsin [Pyrocystis lunula]
MAPIPDGFTYGQWSLVYNSLSFGIAGMGCATIFFWLQLPNVSKSYRTALTITGLVTAIATYHYVRIFNSW
VDAFKVVNVNGGDYTVTLLGAPFNDAYRYVDWLLTVPLLLIELILVMKLPKAETVKLSWNLGVASAVMVA
LGYPGEIQDDLLVRWFWWAMAMIPFYYVVVTLVNGLSDATAKQPDSVKSLVVTARYLTVISWLTYPGV

>gi|6319528|ref|NP_009610.1| Homolog to HSP30 heat shock protein Yro1p; Yro2p [Saccharomyces cerevisiae]
MSDYVELLKRGGNEAIKINPPTGADFHITSRGSDWLFTVFCVNLLFGVILVPLMFRKPVKDRFVYYT
PNLFMSIAYFTMASNLGWIPVRAKYNHVQTSTQKEHPGYRQIFYARYVGWFLAFPWPIIQMSLLG
QIAFNVGMTEIFTVCWLIAACVHSTYKWGYYTIGIGAAIVVCISLMTTTFNLVKARGKDVSNVFIT

Similar tools

• NextGen SFF/FastQ Workbench is an efficient and easy to use FastQ/SFF file viewer, editor, filter and converter.
• Sequence Dereplicator is a tool that allows you to dereplicate your Fasta sequences via sequence clustering.
• NCBI BLAST DB Downloader is a a freeware biology software tool that automates the NCBI BLAST DB download process.

Feedback/News list

This tool is . Please let us know how to make it better. We are interested in:

• Feature requests
• Platform you are interested in (Windows, Mac, Linux)
• Statistics about your files (file type, how many, file size) and your working station (CPU/RAM)
• A name for the program :)