About Pairwise Local Sequence Alignment Tools:
As their name indicates, pairwise local sequence alignment tools are used to find regions of similar or identical sequence between a pairs of DNA, RNA or protein sequences.
Common uses would be to align pairs of either protein or DNA sequence mutants. These programs are also very useful for aligning and comparing DNA sequencing data with the sequence of a known gene or a parental DNA template.
EMBOSS Water
Pairwise sequence alignment using a modified Smith-Waterman algorithm. Sequence pairs should be provided in either GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot format.
Water for Protein or Nucleic Acid Sequences
EMBOSS Matcher
Pairwise sequence alignment based on the LALIGN application. Sequence pairs should be provided in either GCG, FASTA, EMBL, GenBank, PIR, NBRF, Phylip or UniProtKB/Swiss-Prot format.
About Clustal Omega:
Clustal Omega is a multiple sequence alignment tool best used for aligning similar sequence regions between three or more RNA, DNA or protein sequences. For many years, the previous version of the tool, Clustal W, was widely used for this kind of multiple sequence alignment. Clustal Omega is an improved version of that tool.
Accepted sequence formats are GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot. The current version of the software accepts a maximum of 4000 sequences. Uploaded sequence files are limited to a maximum of 4 MB.
Hosted Web Servers:
The application can be used online via hosted web servers at the following locations:
Clustal Omega (Web Server at EMBL-EBI)
Clustal Omega Help (EMBL-EBI FAQ Page)
Clustal Omega (Web Server at Pasteur Mobyle Portal)
Downloading the Application to Your Personal Computer:
The Clustal Omega program can also be downloaded for stand alone use on personal computers running Mac, Windows or Linux operating systems from the following location:
Downloading the JalView Sequence Alignment Results Viewer:
Although Clustal Omega provides a serviceable text-based display of alignment results, the JalView alignment results viewer provides a much nicer way to do it. You can download the appropriate application installer from here:
JalView Desktop/Laptop Downloads
References:
Sievers F, Söding J, Thompson JD, Higgins DG, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R et al. . 2011. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular systems biology 7(1):1-6.
About the Basic Local Alignment Search Tool (BLAST):
The Basic Local Alignment Search Tool (BLAST) allows you to perform local alignments between a user-provided DNA, RNA or protein sequence and the sequences containined in a large number of curated sequence databases (e.g. assembled genome sequences, expressed sequence tags (ESTs), NCBI genomes, patented protein sequences, protein database (pdb) proteins, etc.).
The BLAST suite provides separate interfaces for many different querry sequence/database comparisons. The most commonly used alignment tools are provided with descriptions and links below:
BLAST-N (Nucleotide Querry vs. Nucleotide Sequence DB BLAST)
A user-provided nucleotide sequence is compared against a selected nucleotide sequence database.
BLAST-P (Protein Querry vs. Protein Sequence DB BLAST)
A user-provided protein sequence is compared against a selected protein sequence database.
BLAST-X (Nucleotide Querry → 6 Frame Translation vs. Protein Sequence DB BLAST)
A user-provided nucleotide sequence is used to generated protein sequences from an in silico 6 frame translation. Each of the resulting six protein sequences is compared against a selected protein sequence database.
TBLAST-N (Protein Querry vs. 6 Frame Translation of a Nucleotide Sequence DB BLAST)
A user provided protein sequence is compared against the protein sequences resulting from the in silico 6 frame translation of a selected nucleotide sequence database.
A user-provided nucleotide sequence is used to generated protein sequences from an in silico 6 frame translation. Each of the resulting six protein sequences is compared against the protein sequences resulting from the in silico 6 frame translation of a selected nucleotide sequence database. So although both the initial querry and the comparison database are nucleotide sequences, TBLAST-X results are provided as protein sequence alignments.