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How can I speed up my Blastp?
To speed it up, besides playing “–word_size” as suggested by Corinna, you may also translate your nucleotide sequences to amino acid sequences if possible and switch to BLASTP, or seperate your query sequences into parts and run BLAST+ for each part on same or different computers.
How do you do a Blastp?
Access the “Protein–protein BLAST (blastp)” page by clicking on the link, paste in the query sequence, select the Swissprot database from the “Choose database” pull down menu and click on the BLAST! link. For each protein–protein search, the query is also searched against the Conserved Domain Database (see Note 5).
How do you do a blast with multiple sequences?
How to: Submit multiple query sequences in a single BLAST search
- Choose the appropriate BLAST service from the BLAST Homepage.
- Enter NCBI sequence identifiers (accession numbers, gi numbers) or FASTA-formatted sequences in the appropriate text box.
How does BLAST compare two sequences?
To compare sequences, check the box next to Align two or more sequences under the Query Sequence box. To BLAST the modern human mitochondrial genome sequence (NC_012920.
How often does blast miss a short sequence?
Blast is not guaranteed to find all occurrences of a short sequence in a database. Statistically, even with the word size set to 7 (the minimum for DNA searches) BLAST will typically miss 40% of possible hits when dealing with sequences of 20bp.
Can you use blast to search for short DNA sequences?
Users should be aware that there are issues with BLAST when searching for short sequences. Blast is not guaranteed to find all occurrences of a short sequence in a database. Statistically, even with the word size set to 7 (the minimum for DNA searches) BLAST will typically miss 40% of possible hits when dealing with sequences of 20bp.
Can you blast a 20bp DNA sequence?
Statistically, even with the word size set to 7 (the minimum for DNA searches) BLAST will typically miss 40% of possible hits when dealing with sequences of 20bp. In addition to potentially missing a large percentage of possible matches, any matches Blast does produce will be local alignments rather than full length matches.
How are query sequences given in blast Quickstart?
BLAST “query” sequences are given as character strings of single letter nucleotide or amino acid codes, preceded by a definition line, beginning with a “>” symbol and containing identifiers and descriptive information.