Is BLAST a protein database?

Is BLAST a protein database?

The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

How do you find homologous proteins in BLAST?

A PROTEIN SEQUENCE

1. Go to the BLAST home page and click “protein blast” under Basic BLAST.
2. Paste the sequence in the query box.
3. Enter the name of the organism of interest in the “Organism” box. Click the BLAST button.
4. Click on the desired record and continue at step 2 under “a protein accession number” above.

What database does BLAST use?

BLAST databases are constructed from concatenated FASTA formatted sequences using a program called “formatdb” that produces a mixture of binary- and ascii-encoded files containing the sequences and indexing information used during the BLAST search.

How do you get ortholog?

To find orthologs enter a gene symbol (e.g. RAG1) or a gene symbol combined with a taxonomic group (e.g. primate RAG1). Select the matching entry from the suggestions menu or you can select the orthologs option (e.g. Rag1 orthologs) to see all orthologs.

What is ortholog and paralog?

Orthologs are genes related via speciation (vertical descent), whereas paralogs are genes related via duplication (23). The combination of speciation and duplication events, along with HGT, gene loss, and gene rearrangements, entangle orthologs and paralogs into complex webs of relationships.

What is the difference between BLAST and Psi-BLAST?

PSIBLAST uses position-specific scoring matrices (PSSMs) to score matches between query and database sequences, in contrast to BLAST which uses pre-defined scoring matrices such as BLOSUM62.

What is a Psi-BLAST?

PSI-BLAST (Position-Specific Iterative Basic Local Alignment Search Tool) derives a position-specific scoring matrix (PSSM) or profile from the multiple sequence alignment of sequences detected above a given score threshold using protein–protein BLAST.

What is an ortholog?

Ortholog Identification. Orthologs are defined as genes in different species that have evolved through speciation events only. Paralogs, on the other hand arise by duplication events [2].

What is protein BLAST?

protein blast or blastp. Compares an amino acid query sequence against a protein sequence database. blastx. Compares a nucleotide query sequence translated in all reading frames against a protein sequence database. You could use this option to find potential translation products of an unknown nucleotide sequence.

How do you know if you have ortholog?

The basic procedure entails collecting all the genes in two species and comparing them all to one another. If genes from two species identify each other as their closest partners then they are considered orthologs.