How to run local Blast against a custom database

How to run local Blast against a custom database

Blast2GO allows you to create your own Blast database from a single or multi-species FASTA file using the option “Make Blast Database“. Once the database is formatted it can be used to run a local Blast.

In this demo, we will load 1000 mouse contigs obtained from an RNAseq experiment. We will download EST mouse sequences in fasta format from the NCBI FTP and format them to generate an EST database in Blast2GO. Finally, we will blast our contigs against this database using local Blast. We will also show how to visualize the results and generate several summary charts.

For more video tutorial have a look at our Video Blog or visit our YouTube channel.


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