| LAST finds similar regions between sequences. The main technical innovation is that LAST finds initial matches based on their multiplicity, instead of using a fixed length (e.g. BLAST uses 11-mers). To find these variable-length matches, it uses a suffix array (inspired by Vmatch). To achieve high sensitivity, it uses a spaced suffix array (or subset suffix array), analogous to spaced seeds (or subset seeds). LAST can: - Handle big sequence data, e.g: - Compare two vertebrate genomes. - Align billions of DNA reads to a genome. - Indicate the reliability of each aligned column. - Use sequence quality data properly. - Compare DNA to proteins, with frameshifts. - Compare PSSMs to sequences. - Calculate the likelihood of chance similarities between random sequences. - Do split and spliced alignment. - Train alignment parameters for unusual kinds of sequence (e.g. nanopore). |
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/last
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences. | 1205+galaxy1 | 20.01 | |
| read MAF-format alignments and write them in another format. | 1205+galaxy1 | 20.01 | |
| prepares sequences for subsequent comparison and alignment using lastal. | 1205+galaxy1 | 20.01 | |
| finds local alignments between query sequences, and reference sequences. | 1205+galaxy2 | 20.01 | |
| finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA). | 1205+galaxy1 | 20.01 | |