What is the difference between Phi-BLAST and Psi-Blast?

PSI-BLAST considers position-specific information when searching for significant hits. PHI-BLAST uses a pattern, or profile, to seed an alignment, which is then extended by the normal BLASTP algorithm.

What is masking in BLAST?

Masking is a procedure that identifies low-complexity sequence. See also masking options. Low-complexity sequences are simple repeats such as ATATATATAT or regions that are highly enriched for just one letter, e.g. AAACAAAAAAAAGAAAAAAC.

What is Phi-BLAST used for?

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

What is Fasta NCBI?

Website. www.ncbi.nlm.nih.gov/BLAST/fasta.shtml. In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes.

What is BLAST evalue?

The BLAST E-value is the number of expected hits of similar quality (score) that could be found just by chance. E-value of 10 means that up to 10 hits can be expected to be found just by chance, given the same size of a random database.

Why do we mask repeats?

Repetitive sequence is found throughout genomes. It is important to mask repeats before gene annotation, as repeats will cause non-specific gene hits. Repeats are also useful for studying evolution and for DNA fingerprinting.

What is hard masking in bioinformatics?

Masked reference genomes are also known as hard-masked DNA sequences. Repetitive and low complexity DNA regions are detected and replaced with ‘N’s. The use of masked genome may adversely affect the analysis results, leading to wrong read mapping and incorrect variant calls.

What is difference between FASTA and BLAST?

The main difference between BLAST and FASTA is that BLAST is mostly involved in finding of ungapped, locally optimal sequence alignments whereas FASTA is involved in finding similarities between less similar sequences.

What is the E value in BLAST?

The Expect value (E) is a parameter that describes the number of hits one can “expect” to see by chance when searching a database of a particular size. It decreases exponentially as the Score (S) of the match increases. Essentially, the E value describes the random background noise.

What is the difference between BLASTp and blastpgp?

blastpgp is the program used to run PSI-BLAST and PHI-BLAST. These programs are specialized protein BLAST comparisons that are more sensitive than the standard BLASTP search. PSI-BLAST considers position-specific information when searching for significant hits.

What’s the default parameter for PSI BLAST in blastpgp?

To run PSI-BLAST, the – j parameter must be set to something greater than 1. The default of – j 1 means that there are no iterations and that it’s therefore the same as a single BLASTP search. Setting – j sets the maximum number of iterations to run, with the program stopping beforehand if the search comes to convergence.

How to create a PSSM file in PSI-BLAST?

The PSSM, or checkpoint file, is created internally by PSI-BLAST, but it can also be exported to a file using the -C option of blastpgp. This option is extremely useful. You can use the checkpoint file in subsequent PSI-BLAST ( blastpgp) searches or as a database entry for the RPS-BLAST program.

How to use the checkpoint file in blastall?

You can use the checkpoint file in subsequent PSI-BLAST ( blastpgp) searches or as a database entry for the RPS-BLAST program. You can also use the PSSM in a specialized tblastn search in blastall by using the – p psitblastn and – R options with a nucleotide database.