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Bio::Tools::Run::PiseApplication::fasta 1.4

  Date Added: October 24, 2010  |  Visits: 364

Bio::Tools::Run::PiseApplication::fasta

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Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search. Parameters: fasta (Excl) Fasta program query (Sequence) Query sequence File pipe: seqfile seqtype (Excl) Is it a DNA or protein sequence (-n) protein_db (Excl) Protein Database nucleotid_db (Excl) Nucleotid Database break_long (Integer) Break long library sequences into blocks (-N) ktup (Integer) ktup : sensitivity and speed of the search (protein:2, DNA:6) optcut (Integer) OPTCUT : the threshold for optimization. (-c) gapinit (Integer) Penalty for gap initiation (-12 by default for fasta with proteins, -16 for DNA) (-f) gapext (Integer) Penalty for gap extention (-2 by default for fasta with proteins, -4 for DNA) (-g) high_expect (Float) Maximal expectation value threshold for displaying scores and alignments (-E) low_expect (Float) Minimal expectation value threshold for displaying scores and alignments (-F) nucleotid_match (Integer) Reward for a nucleotid match (-r) nucleotid_mismatch (Integer) Penalty for a nucleotid mismatch (-r) matrix (Excl) Scoring matrix file (-s) X_penalty (Integer) Penalty for a match to X (independently of the PAM matrix) (-x) frameshift (Integer) Penalty for frameshift between codon (fast[xy]/tfast[xy])(-h) frameshift_within (Integer) Penalty for frameshift within a codon (fasty/tfasty)(-j) threeframe (Switch) Search only the three forward frames (tfasta) (-3) invert (Switch) Reverse complement the query sequence (all tfasta) (-i) genetic_code (Excl) Use genetic code for translation (tfasta/tfast[xy]/fast[xy]) (-t) band (Integer) band-width used for optimization (-y) swalig (Switch) unlimited Smith-Waterman alignment for DNA (-A) noopt (Switch) no limited optimization (-o) stat (Excl) Specify statistical calculation. (-z) random (Switch) Estimate stat parameters from shuffled copies of each library sequence (-z) histogram (Switch) No histogram (-H) scores (Integer) number of similarity scores to be shown (-b) alns (Integer) number of alignments to be shown (-d) html_output (Switch) HTML output (-m) markx (Excl) Alternate display of matches and mismatches in alignments init1 (Switch) sequences ranked by the z-score based on the init1 score (-1) z_score_out (Excl) Show normalize score as (-B) showall (Switch) both sequences are shown in their entirety in alignments (fasta only) (-a) linlen (Integer) output line length for sequence alignments (max. 200) (-w) offsets (String) Start numbering the aligned sequences at position x1 x2 (2 numbers) (-X) info (Switch) Display more information about the library sequence in the alignment (-L) statfile (OutFile) Write out the sequence identifier, superfamily number, and similarity scores to this file (-R) filter (Switch) Lower case filtering (-S) outfile (OutFile) pipe: mview_input html_outfile (OutFile).

Requirements: No special requirements
Platforms: Linux
Keyword: Alignments,  Biotoolsrunpiseapplicationfasta,  Dna,  Excl,  Integer,  Libraries,  Outfile,  Penalty,  Piseapplication,  Programming,  Sequence,  Sequence Database,  Switch
Users rating: 0/10

License: Freeware Size: 82.94 KB
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