What is a Phi-BLAST?

PHI-BLAST (Pattern-Hit Initiated BLAST) is a search program that combines matching of regular expressions with local alignments surrounding the match.

What are the different types of BLAST?

The five traditional BLAST programs are: BLASTN, BLASTP, BLASTX, TBLASTN, and TBLASTX. BLASTN compares nucleotide sequences to one another (hence the N). All other programs compare protein sequences (see Table 5-1).

What is the difference between Blastn and Tblastn?

Blastx will search your sequence in a protein database with a nucleotide sequence as input while tblastn will search in a nucleotide database with a protein input.

What is the best e value in BLAST?

Blast hits with an E-value smaller than 1e -50 includes database matches of very high quality. Blast hits with E-value smaller than 0.01 can still be considered as good hit for homology matches.

What does PSI BLAST do?

Position-Specific Iterative (PSI)-BLAST is a protein sequence profile search method that builds off the alignments generated by a run of the BLASTp program. In the evolution, three-dimensional (3D) structures of proteins may be conserved even after considerable erosion of their sequence similarity.

How do you run Phi BLAST?

In given link perform following steps :

1. Enter accession number(s), gi(s), or FASTA sequence(s) or upload the sequence.
2. choose database and organism.
3. Choose Program – PHI BLAST (it is probably third option)
4. Perform BLAST by clicking BLAST button.

Why do we use BLAST?

BLAST is a powerful tool used to search a database of DNA or protein sequences in order to find “hits” that are similar to a query sequence.

How many genomes are available on BLAST?

This tool, available at the NCBI web site http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/genom_table_cgi, currently provides access to over 170 bacterial and archaeal genomes and over 40 eukaryotic genomes.

What is the function of BLAST?

BLAST is a computer algorithm that is available for use online at the National Center for Biotechnology Information (NCBI) website, as well as many other sites. BLAST can rapidly align and compare a query DNA sequence with a database of sequences, which makes it a critical tool in ongoing genomic research.

How do you save primer blast results?

Q: Saving your search parameters You can also save the search, if logged into My NCBI, which will save that search strategy. To save, click on the “[Save Search Strategies]” link near the top of the blast results page.

How do you save blast results?

The results of a BLAST search can be displayed as either a Hit Table or a Query Centric alignment. To export the results of a single Hit table (ie the results of a single BLAST search), select all the entries in the document table that you wish to export and selecting File -> Export -> Selected Documents.