NAME

GeneDesign::Basic - perl functions for computer assisted synthetic design

VERSION

Version 3.00

DESCRIPTION

GeneDesign is a library for the computer-assisted design of synthetic genes

Functions

define_aa_defaults() Generates a hash. KEYS: one letter amino acid code (string) VALUES: most highly expressed codon for that amino acid (string) in: reverse codon table (hash reference), RSCU value table (hash reference) out: amino acid default table (hash)

define_codon_table() Generates a hash. KEYS: codons (string) VALUES: amino acids (string) in: switch for codon table (1) out: codon table (hash)

define_reverse_codon_table() Generates a reference to a hash. KEYS: amino acids (string) VALUES: codon list (array reference) in: codon table (hash reference) out: reverse codon table (hash)

define_RSCU_values() Generates a hash. KEYS: codons (string) VALUES: RSCU value (float) in: switch for species (1 s.cer, 2 e.col, 3 h.sap, 4 c.ele, 5 d.mel) out: RSCU value table (hash)

RSCU_filter() Deletes anything from the RSCU_TABLE that doesn't meet minimum RSCU. in: rscu table (hash reference), minimum RSCU value (integer) out: rscu table (hash reference)

define_codon_percentages() Generates a hash. KEYS: codons (string) VALUES: RSCU value over codon family size (float) in: codon table (hash reference), RSCU value table (hash reference) out: codon percentage table (hash)

index_codon_percentages() Generates two arrays for x and y values of a graph of codon percentage values. in: dna sequence (string), window size (integer), codon percentage table (hash reference) out: x values (array reference), y values (array reference)

pattern_remover() takes a nucleotide sequence, a nucleotide "pattern" to be removed, and a few codon tables, and returns an edited nucleotide sequence that is missing the pattern (if possible). Ranks codon replacements by RSCU differences to minimize expression damage. in: nucleotide sequence (string), nucleotide pattern (string), codon table (hash reference), RSCU value table (hash reference) out: nucleotide sequence (string) OR null

pattern_adder() takes a nucleotide sequence, a nucleotide "pattern" to be interpolated, and the codon table, and returns an edited nucleotide sequence that contains the pattern (if possible). in: nucleotide sequence (string), nucleotide pattern (string), codon table (hash reference), RSCU value table (hash reference) out: nucleotide sequence (string) OR null

pattern_aligner() takes a nucleotide sequence, a pattern, a peptide sequence, and a codon table and inserts Ns before the pattern until they align properly. This is so a pattern can be inserted out of frame. in: nucleotide sequence (string), nucleotide pattern (string), amino acid sequence (string), codon table (hash reference) out: nucleotide pattern (string)

pattern_finder()

change_codons() takes a nucleotide sequence and a few codon tables and tries to recode the nucleotide sequence to one of four algorithms, 0 random, 1 most optimal, 2 next most optimal, 3 most different, 4 least different. in: nucleotide sequence (string), codon table (hash reference), reverse codon table (hash reference), RSCU value table (hash reference), algorithm number tag: try not to change the first two bases of the first codon in. out: nucleotide sequence (string)

reverse_translate() takes an amino acid sequence and a specific codon table and returns that frame translated into amino acids. See gdRevTrans.cgi for use. in: nucleotide sequence (string), switch for frame (1, 2, or 3), codon table (hash reference) out: amino acid sequence (string)

amb_transcription() takes an ambiguous nucleotide sequence and returns a list of all possible non ambiguous nucleotide sequences it could represent in: nucleotide sequence (string), codon table (hash reference), reverse codon table (hash reference) out: nucleotide sequence list (vector)

amb_translation() takes a nucleotide that may be degenerate and a codon table and returns a list of all amino acid sequences that nucleotide sequence could be translated into. in: nucleotide sequence (string), codon table (hash reference) out: amino acid sequence list (vector)

degcodon_to_aas() takes a codon that may be degenerate and a codon table and returns a list of all amino acids that codon could represent. If a hashref is provided with previous answers, it will run MUCH faster. in: codon (string), codon table (hash reference) out: amino acid list (vector)

translate() takes a nucleotide sequence, a frame, and a codon table and returns that frame translated into amino acids. in: nucleotide sequence (string), switch for frame (±1, ±2, or ±3), codon table (hash reference) out: amino acid sequence (string)

codon_count() takes a reference to an array of sequences and returns a hash with codons as keys and the number of times the codon occurs as a value. in: gene sequence (array reference) out: codon count (hash reference)

generate_RSCU_values() takes a hash reference with keys as codons and values as number of times those codons occur (it helps to use codon_count) and returns a hash with each codon and its RSCU value in: codon count (hash reference), reverse codon table (hash reference) out: RSCU values (hash reference)

rscu_parser() takes the form AAA (K) 0.540

AUTHOR

Sarah Richardson <notadoctor@jhu.edu>.

COPYRIGHT AND LICENSE

Copyright (c) 2011, GeneDesign developers All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the Johns Hopkins nor the names of the developers may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE DEVELOPERS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

cpanm Bio::GeneDesign::Basic

perl -MCPAN -e shell
install Bio::GeneDesign::Basic