After downloading the EST genomic database from NCBI GenBank (downloaded from ftp blast databases from NCBI as EST-others, at ftp://ftp.ncbi.nih.gov/blast/db/FASTA/)
1. How could I convert the files in the .tar folder into FASTA format that is usable by an in-house Mascot server? There are a bunch of files in the folder in different types (e.g.: .nsq, nhr, nin, etc). Do I need to use all of them?
2. What should I do to create the usable translated information (e.g. FASTA protein sequence) from such downloaded EST database?
3. Do I need to manually annotate the entires of a species?
ftp://ftp.ncbi.nih.gov/blast/db/FASTA/
Tpically EST sequences are translated in all six frames to get the peptde sequences which you can search then using typical search engines like Mascot/Sequest. Alternatively you can ty to get a single protein sequence from an EST using software like ESTScan
You can have a look at Peppy too, if it serves your purpose:
http://www.ncbi.nlm.nih.gov/pubmed/23614390
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics