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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. 

Feature Status ETA

Send queries to NCBI BLAST server



Retrieve result page from NCBI BLAST server



Automatically download GBK files



Perform eLink, eSearch

Done. To be incorporated


Show results table

In progress


Let user sort the table

In progress


Show alignments

Not ready


Integrates with DNA Sequence Assembler

Not ready


Analyze results

Not 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.


Visual FastQ file viewer & converter


FastQ dereplicate



NCBI Blaster

Download time

under 10 seconds

Sequence Workbench is now part of the Avalanche NextGen package. Please download this package.


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



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]

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




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Feedback/News list


This tool is Nextgen SFF/fastq analysis software. 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 :)


SFF to FastQ to FASTA converter