Can you BLAST Fastq files?
You can’t use a fastq format file to do blast. Convert to fasta format before doing search.
What is a BLAST database?
BLAST is an acronym for Basic Local Alignment Search Tool and refers to a suite of programs used to generate alignments between a nucleotide or protein sequence, referred to as a “query” and nucleotide or protein sequences within a database, referred to as “subject” sequences.
Why do you create BLAST database?
The BLAST program scans the database sequences for the remaining high-scoring word, such as PEG, of each position. If an exact match is found, this match is used to seed a possible un-gapped alignment between the query and database sequences. Extend the exact matches to high-scoring segment pair (HSP).
How do you create a protein database?
Navigate to the Protein Sequence Database Utilities page, and select the Create or append user database option….Create or Append to a Database Containing User Supplied Protein
- Type the database name.
- Type a description for the database entry.
- Type a species for the entry.
- Type an accession number for the entry.
How to create a BLAST database in formatdb?
You may specify that input come from stdin with -i stdin, but you must also set the -n parameter to give it a name. If you wish to make a single BLAST database from multiple FASTA files, pipe them to formatdb as follows: Specifies an output log file. Log messages are appended to this file. Creates an alias database, which has several uses.
Where can I find the database for blast?
BLAST databases are updated daily and may be downloaded via FTP from ftp://ftp.ncbi.nlm.nih.gov/blast/db/. Database sets may be retrieved automatically with update_blastdb.pl, which is part of the BLAST+ suite.
How to load local blast.xml into Blast2GO?
Run blast. Load your local_blast.xml file into Blast2GO (File -> Load -> Load Blast Results -> XML files) and visualize several Blast results (Show Blast Results) to see if the accession appears in the right place (ACC). You can proceed with the mapping step as usual.
When to format FASTA file for local blast?
If you intent to use the results later on in Blast2GO or OmicsBox for functional annotation etc. you have to be careful with the formatting because Blast2GO/OmicsBox will need the accession IDs information in order to execute the Gene Ontology mapping for the functional annotation step.