---
name: "plast"
section: "1"
platform: "linux"
package: "plast"
version: "2.3.2+dfsg-10+b6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/plast"
---

# plast(1)

Parallel Local Sequence Alignment Search Tool

## NAME

plast - Parallel Local Sequence Alignment Search Tool

## DESCRIPTION

plast 2.3.1

-

  \- Build date: 2016-02-09 09:47:45 - OS: Linux-4.3.0-1-amd64 - Compiler: */usr/bin/cc* (5.3.1) - Host CPU: 4 cores available

\[\*\] denotes mandatory argument.

- **-p** \[\*\]:

  Program Name \[plastp, tplastn, plastx, tplastx or plastn\]

- **-d** \[\*\]:

  Subject database file

- **-i** \[\*\]:

  Query database file

- **-o** :

  PLAST report Output File

- **-e** :

  Expectation value

- **-n** :

  Size of neighbourhood peforming ungapped extension

- **-s** :

  Ungapped threshold trigger a small gapped extension

- **-g** :

  threshold for small gapped extension

- **-b** :

  bandwidth for small gapped extension

- **-a** :

  Number of processors to use

- **-G** :

  Cost to open a gap

- **-E** :

  Cost to extend a gap

- **-xdrop-ungap** :

  X dropoff value for Ungapped alignment (in bits) (zero invokes default behavior 20 bits)

- **-X** :

  X dropoff value for gapped alignment (in bits) (zero invokes default behavior)

- **-Z** :

  X dropoff value for final gapped alignment in bits (0.0 invokes default behavior)

- **-index-threshold** :

  Index threshold to calculate the similarity between neighbour

- **-F** :

  Filter query sequence

- **-M** :

  Score matrix (BLOSUM62 or BLOSUM50)

- **-strand** :

  strands for plastn: 'plus', 'minus' or 'both' (default)

- **-r** :

  reward for a nucleotide match (plastn)

- **-q** :

  penalty for a nucleotide mismatch (plastn)

- **-force-query-order** :

  Force queries ordering in output file.

- **-max-database-size** :

  Maximum allowed size (in bytes) for a database. If greater, database is segmented.

- **-max-hit-per-query** :

  Maximum hits per query. 0 value will dump all hits (default)

- **-max-hsp-per-hit** :

  Maximum alignments per hit. 0 value will dump all hits (default)

- **-outfmt** :

  Output format: 1 for tabulated (default), 2 for extended tubulated, 4 for NCBI Blast-like.

- **-strands-list** :

  List of the strands (ex: "1,2,6") to be used when using algo using nucleotids databases.

- **-optim-codon-stop** :

  size of the allowed range between the last invalid character and the next stop codon

- **-factory-dispatcher** :

  Factory that creates dispatcher.

- **-factory-statistics** :

  Factory that creates statistics builder.

- **-factory-indexation** :

  Factory that creates indexation builder.

- **-factory-hit-ungap** :

  Factory that creates ungap hits iterator.

- **-factory-hit-smallgap** :

  Factory that creates small gap hits iterator.

- **-factory-hit-fullgap** :

  Factory that creates full gap hits iterator.

- **-factory-hit-composition** :

  Factory that creates composition hits iterator.

- **-factory-gap-result** :

  Factory that creates gap alignments result.

- **-factory-ungap-result** :

  Factory that creates ungap alignments result.

- **-splitter** :

  Factory that creates an alignment splitter. String: 'normal' or 'banded' (default)

- **-optim-filter-ungap** :

  Optimization that filters out through ungap alignments.

- **-bargraph** :

  Display a progress bar during execution.

- **-bargraph-size** :

  Nb of characters of the bargraph.

- **-progression-file** :

  Dump in a file the current execution percentage.

- **-verbose** :

  Display information during algorithm execution.

- **-full-stats** :

  Dump algorithm statistics.

- **-stats** :

  Dump generic statistics.

- **-stats-fmt** :

  Format of statistics: 'raw' (default) or 'xml'

- **-stats-auto** :

  Automatic stats file creation

- **-alignment-progress** :

  Dump in a file the growing number of ungap/ungap alignments during algorithm.

- **-resources-progress** :

  Dump in a file information about resources during algorithm.

- **-plastrc** :

  Pathname of the plast config file.

- **-xmlfilter** :

  Uri of a XML filter file.

- **-seeds-use-ratio** :

  Ratio of seeds to be used.

- **-seeds-index-filter** :

  seeds length to be used for the indexation filter.

- **-complete-subject-database-stats-file** :

  File path to the stats of the complete subject database

- **-W** :

  size of the seeds

- **-h** :

  help

Citing PLAST: Nguyen VH, Lavenier D. (2009) PLAST: parallel local alignment search tool for database comparison. BMC Bioinformatics, vol 10, no 329.

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.