BioPHP: PHP for Biocomputing

BioPHP's Place in the Universe top


On to the question of what it can do. At the moment, BioPHP focuses on sequence analysis and sequence alignment. The table below summarizes BioPHP's functionality.

Classification of BioPHP Classes and Methods by Functional Area

Functional Area in Bioinformatics BioPHP classes and methods
1) Querying/Parsing data from biological files/databases.


   a) Local files/databases

SeqDB class: parse_id, parse_swissprot, at_entrystart, close, fetch, first, last, prev, next, get_entryid, isa_qualifier, open

RestEn class: FindRestEn, GetCutPos, GetLength, GetPattern

Seq: count_codons, get_codon

   b) Remote files/databases

(None yet)

2) Sequence analysis  
   a) Manipulating sequences RestEn: CutSeq
Seq: expand_na, subseq, trunc
   b) Analyzing sequences

Protein: seqlen, molwt

Seq: charge, chemgrp, complement, molwt, revcomp, seqlen, patfreq, symfreq, translate, translate_codon

   c) Predicting Gene Locations (None yet)
   d) Feature/pattern detection Seq: find_mirror, find_palindrome, findpattern, getbridge, halfstr, is_mirror, is_palindrome, patpos, patposo,
   e) Measuring sequence similarity

SeqMatch: compare_letter, hamdist, levdist, match, partial_match, xlevdist

SubMatrix: addrule

3) Pairwise alignment
(None yet)
4) Multiple sequence alignment


   a) Querying/parsing an alignment set, member sequences SeqAlign: char_at_res, fetch, first, last, next, prev, substr_bw_res
   b) Manipulating an alignment set, member sequences SeqAlign: add_seq, del_seq, select, sort_alpha, subalign
   c) Analyzing an alignment set, member sequences SeqAlign: consensus, col2res, get_gap_count, get_is_flush, get_length, res2col, res_var
5) Phylogenetic Analysis (None yet)
6) Protein Structure Analysis (None yet)
7) Protein Structure Prediction (None yet)
8) Protein Visualization (None yet)

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Copyright © 2003 by Sergio Gregorio, Jr.
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