5 Server for Batch BLAST against NCBI database

BLAST has become an indispensable tool for the biological research. in the genomic era, you cann't do anything with BLAST especially when volume of data is increasing day by day. Although there several good servers are there to BLAST single sequences, services for batch BLAST or facility of using many query sequences is still very limited. in this post, we will look for the different services for batch BLAST analysis.


1. NCBI BLAST : NO doubt, this is the best database or you may say mother of all databases. NCBI provide option for batch BLAST but it's limited to 50 query sequences. to query multiple sequences. To use NCBI to query for batch BLAST, go to their BLAST page, paste or upload your query sequences like this

Since, your output will be very large so you may prefer to choose tabulated version of output of NCBI blast and you are done.

2. University of ChicagoDr. Liu's Laboratories at University of Chicago provides a server of batch BLAST. Basically it is web implementation of NCBI's Blastcl3 softwares. There is no limitation for number of queries sequences like NCBI BLAST here.

3. PlantGDB BLAST : PlantGDB is an exclusive database for plant genomes and therefore you can use this server for batch BLAST with plant genomes only. Number of query per file is limited to 100 for this web server. 

4. Aertifical life and other intelligence : I never use this server but it looks promising if you have own database then it can help you.

5. GreenGene : Greengene is my first choice for batch BLAST analysis for unlimited sequences. If you are really interest in BATCH blast against NCBI database, you must give a try to Green Gene. In fact you can use their batch BLAST output parser HERE to analyse you result also

P.S. You may also like to give a try to microgen BLASTOR from here

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