NCBI Protein Blast

BLASTX search protein databases using a translated nucleotide query.

TBLASTX search translated nucleotide database using a translated nucleotide query.

TBLASTN search translated nucleotide database using a protein query.

Compares a protein sequence or a protein profile HMM to a DNA sequence, allowing for introns and frameshifting errors. The software can also be downloaded.

NCBI BLAST2 on varied protein databases

WU-BLAST2 stands for Washington University Basic Local Alignment Search Tool Version 2.0. The emphasis of this tool is to find regions of sequence similarity quickly, with minimum loss of sensitivity. Online query tool from the EBI. Also allow serach of the Alternative Splicing Database (ASD)

Position specific iterative BLAST (PSI-BLAST) constructs a profile automatically from the first set of BLAST alignments. PSI-BLAST is similar to NCBI-BLAST2 except that it uses position-specific scoring matrices derived during the search, this tool is used to detect distant evolutionary relationships. Online tool at EBI.

Pattern Hit Initiated BLAST (PHI-BLAST) treats two occurrence of the same pattern within the query sequence as two independent sequences. This can be seen in a number of ways, from the statistical analysis at the end of the search results. This tool is only available for database protein searches. Onine tool provided by EBI.

Nucleotide Similarity Search. EBI services that provides sequence similarity search against nucleotide and protein databases using the FASTA programs. FASTA can be very specific when identifying long regions of low similarity especially for highly diverged sequences. Works also for full genomes. Software can be downloaded.

EBI service tool that provides sequence similarity searching against complete proteomes databases using the FASTA programs.

Scan Protein Sequence (ScanPS) is a program for comparing a protein sequence to a database of protein sequences. It implements the full Smith-Waterman style searching and is capable of identifying multiple domain matches by using iterative profile searching.

MPsrch is a biological sequence sequence comparison tool that implements the true Smith and Waterman algorithm. It allows an rigorous search using an exhaustive algorithm, which is recognised as the most sensitive sequence comparison method available, and is capable of identifying hits in cases where BLAST and FASTA fail and also reports fewer false-positive hits.

SHOPS (SHow OPeron Structures) analyzes the genomic operon context for any group of proteins selected on the basis of a set of sequence or domain identifiers. It uses genome annotations of all available fully sequenced prokaryotes to create a scaled graphical overview of the genomic context around the proteins of interest.