## Local pairwise sequence alignment

### Description

Waterman-Eggert local alignment of two sequences

This tool runs EMBOSS command matcher that identifies local similarities in two input sequences using a rigorous algorithm based on Bill Pearson's lalign application, version 2.0u4 (Feb. 1996). The substitution matrix, gap insertion and extension penalty are specified. The specified number of top-scoring pair-wise local sequence alignments are written to file.

The input sequences can be in any of the EMBOSS compatible sequence formats.

For more details, please check the manual page of getorf command.

### Parameters

- How many alignments to showThis sets the number of alternative matches output. By default only the highest scoring alignment is shown. A value of 2 gives you other reasonable alignments. In some cases, for example multidomain proteins of cDNA and genomic DNA comparisons, there may be other interesting and significant alignments.
- Gap penalty Gap penalty
- Gap length penalty Gap length penalty
- Scoring matrix Choose the scoring matrix file used when comparing sequences. By default BLOSUM62 (for proteins\) or the file EDNAFULL (for nucleic sequences\) are used)
- Output type for outfile Choose format for output file

### Output

Output is a fasta formatted sequence file.