plast1

Overview

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.