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BioPHP - Functions

BioPHP - Functions

alignment_of_dna
Alignment of two DNA sequences. 
Smith-Waterman alignment method is used.


alignment_of_proteins
Alignment of two protein sequences. 
Smith-Waterman alignment method is used.


basic_tm
Basic melting (Tm) temperature foroligonucleotides


chemgrp_protein
Translates peptide sequence to checmical groups.


complement
Gets the genetic complement of a DNA or RNA sequence. 


count_codons_dna_or_rna
Counts the number of codons (trios of base-pairs) in a DNA/RNA sequence.


dna_is_palindrome
This is my proposal to substitute is_palindrome function from GenePHP. I
have just tried to make it simple.
By using function RevComp_DNA2 it allows searching within sequences with
degenerated nucleotides
Although its length is not odd, a pattern like TATANTATA will be
considered palindromic
Uses function RevComp_DNA2


dna_remove_non_coding
Removes non coding characters from DNA sequence. Degenerated nucleotides
are not removed.


dna_to_protein
Translates DNA to protein by using one of the 13 genetic codes described.


expand_na
Returns the expansion of a nucleic acid sequence, replacing special
wildcard symbols with the proper PERL regular expression.


find_palindromic_seqs
Searches for palindromic sequences within a DNA sequence.
Length of palindromic sequences to be searched will be between $min and
$max values
Will return an array with key = start position and val= palindromic
sequence

Requires function DNA_is_palindrome


find_tandem_repeats
Searches for tandem repeats  within a DNA sequence.


gc_content
Computes G+C content of DNA sequence


get_bridge
Returns the sequence located between two palindromic halves of a
palindromic string. 
Take note that the \"bridge\" as I call it, is not necessarily a genetic
mirror or a palindrome.



get_oligos_from_pattern
Will response with sequences recognized by a oligo pattern.

If oligo does not include degenerate nucleotides response will be the same
oligo           
      example: oligo is TATA, and response will be TATA                   
               

If oligo includes degenerate nucleotides response will be comma separated
sequences
      example: oligo is WATW, and response will be AATA,AATT,TATA,TATT


halfstr
Returns one of the two palindromic \"halves\" of a palindromic string. 


identify_aminoacid
Returns complete name of aminoacid. Input may be one or three letter code.


molwt_nucleic_acid
Calculates the molecular weight of a nucleic acid.
From GenePHP, seq.php, class seq


molwt_protein
Computes the molecular weight of a protein sequence.


nucleotide_composition
Calculates nucleotide composition of sequences (number of A,C,G,T,N,Y,R...)


nucleotide_identification
Returns name of nucleotide. P.e., for A, returns "Adenosine".
Degenerated nucleotides are also identified. P.e., for R, returns "Purine
(A & G)"


number_of_matching_sequences
Will response number of sequences matching an oligo.
This number will be >1 when degenerated nucleotides are included in the sequence


protein_to_dna
Reverse translation of protein to DNA by using one fo the 13 genomic codes
described.


random_dna
Generates a random DNA sequence. Number of A, C, G and T must be provided. 


revcomp
Gets the complement of a DNA/RNA sequence, and returns it in reverse order.


revcomp_dna
Returns Reverse-Complement of DNA sequence. It is similar to revcomp
function in GenePHP (in etc.php file), but the speed is about 6x faster.


revcomp_dna2
This function is derived from RevComp_DNA function. I think it may be
interesting to maintaing RevComp_DNA and RevComp_DNA2 as two separated
functions; for
big sequences, the functions may be selected depending on needs.

This function allows transforming the sequence when degenerated
nucleotides are present.


salt_adjusted_tm
Salt_Adjusted Melting Temperature (Tm) Calculations
$salt: monovalent cations concentration([K+] + [Na+]), mM



seq_to_pattern_with_uib
Transforms a DNA sequence into a pattern
Example: from RCGY to [AG]CG[CT]


seqlen
Returns the length of a sequence


stats_factorial
Computes factorial of number


stats_mean
Will calculate the mean of a serie of numbers.



stats_regression_correlation
Computes standard curve (y=ax+b) and correlation coefficient (r).


stats_standard_deviation
Calculates Standard Deviation of a serie of numbers


stats_variance
Calculates varience of a serie of numbers


subseq
Return subsequence of sequence based in start and length of subsequence


translate_codon
Translate a codon to correspondin aminoacid.
If $format=3, a three letter aminoacid named is obtained.
If $format=1, a one letter aminoacid named is obtained