blastp
Blastp is a command line tool used for protein sequence similarity searching. It is a part of the widely used Basic Local Alignment Search Tool (BLAST) suite of programs. The tool compares an input protein sequence against a database of protein sequences, searching for similar sequences. Blastp uses a heuristic algorithm that applies local alignment techniques to find regions of similarity between the query sequence and database sequences. It assesses the statistical significance of the alignments using a statistical measure called E-value, which estimates the probability of obtaining a similar alignment by chance. Blastp also generates a bit score that represents the overall similarity of the alignment. The tool provides various output formats, allowing users to view the results in different ways. It is highly customizable and offers a range of options to enhance the sensitivity and specificity of the search. Users can specify parameters such as threshold scores, gap penalties, and substitution matrices to optimize the search results. Blastp is widely used in bioinformatics and plays a crucial role in identifying, annotating, and comparing protein sequences.
List of commands for blastp:
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blastp:tldr:24a68 blastp: Search protein databases using a protein query, 16 threads to use in the BLAST search, with a maximum number of 10 aligned sequences to keep.$ blastp -query ${query-fa} -db ${blast_database_name} -num_threads ${16} -max_target_seqs ${10}try on your machineexplain this command
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blastp:tldr:404b0 blastp: Align two or more sequences, custom tabular output format, output to file.$ blastp -query ${query-fa} -subject ${subject-fa} -outfmt '${6 qseqid qlen qstart qend sseqid slen sstart send bitscore evalue pident}' -out ${output-tsv}try on your machineexplain this command
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blastp:tldr:5466c blastp: Search the remote non-redundant protein database using a protein query.$ blastp -query ${query-fa} -db ${nr} -remotetry on your machineexplain this command
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blastp:tldr:92bca blastp: Align two or more sequences using blastp-fast.$ blastp -task blastp-fast -query ${query-fa} -subject ${subject-fa}try on your machineexplain this command
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blastp:tldr:be4e3 blastp: Display help (use `-help` for detailed help).$ blastp -htry on your machineexplain this command
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blastp:tldr:cbe7a blastp: Align two or more sequences using blastp, with the e-value threshold of 1e-9, pairwise output format, output to screen.$ blastp -query ${query-fa} -subject ${subject-fa} -evalue ${1e-9}try on your machineexplain this command