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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
|
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| 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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