BioPHP: PHP for Biocomputing

Last updated: June 3, 2003

All the scripts were written by Serge Gregorio. Most of the Combo scripts use unreleased BioPHP 1.1 code, while most of the Simple scripts use released BioPHP 1.0 code. Combo scripts use a combination of different BioPHP classes and methods to perform a certain (non-trivial, real world) task. Simple scripts are short scripts written simply to demonstrate the capabilities and proper use of BioPHP classes or methods.

This section is still under development. At the moment, source code listings are available for only a few scripts. While parameter pages have a consistent look and feel, the results pages have not yet been standardized. Please bear with us.

Combo scripts top

Sequence Records Query-by-Example (QBE) Script (50 % complete)

Script that searches for sequence records that meet certain criteria given by user in a QBE-like manner. Still under development. At the moment, you can only specify values for four or so parameters (Accession, Sequence Length, Molecule Type, and Source Organism.

Six-frame Protein Translation Script

Similar to the above Protein Translation Script, except that this generates all six possible reading frame translations instead of just one. In addition to translate() method, this also uses the complement() method of the Seq class.

Six-frame Protein Translation Script Version 2

Similar to the above Six-frame Protein Translation Script, with the output in a slightly different format.

Reverse Protein Translation Script

Accepts a protein (amino acid) sequence in single-letter, non-expanded (alphabet) format, and returns a list of all possible nucleic codons that code for the given protein sequence. This uses the revtrans_aa(), format_aa(), and chk_aa() methods of BioPHP 1.1.

Find a Pair of Restriction Sites in a Sequence (90% complete)

A tool that helps the user select a restriction enzyme with which to cut or extract a target fragment within a larger DNA sequence. Still under development. The result details page (GenBank viewer) does not work yet because of the rather special way Sourceforge handles session variables.

Amateur Gene Finder

Attempts to find the shortest candidate genes within a sequence by looking for pairs of START and STOP codons nearest each other. Caution: The script has not yet been optmized to handle long input sequences. Do not input very long (>8,000 bases) sequences as it takes long (>15 seconds) for the script to execute.

Simple scripts top

Nucleotide Pattern Matching Script

Simple script that lists all sequences that contain a given nucleotide pattern. This makes use of the expand_na() and patposo() methods of the Seq class. The algorithm used is not optimized for large databases.

Charge/Chemgroup String Script [ View source code ]

Simple script that demonstrates the use of charge() and chemgrp() methods of the Seq class.

Sequence Similarity Script

Simple script that demonstrates the use of hamdist() and levdist() methods of the SeqMatch class.

Protein Translation Script [ View source code ]

Simple script that demonstrates the use of the translate() method of the Seq class. It accepts a nucleic acid sequence and translates it into an amino acid sequence.

Find Mirror/Palindrome in a Sequence

Searches for genetic mirrors and palindromes in a given nucleic sequence. Demonstrates the use of the find_mirror() and find_palindrome() methods of the Seq class.

Various Methods of the Seq class

Demonstrates the use of molwt(), complement(), revcomp(), and simpler methods of the Seq class.

Find Fragments from Restriction Enzyme Digest [ View source code ]

Completely digests (cuts) a given nucleotide sequence using a given restriction enzyme.


Copyright © 2003 by Sergio Gregorio, Jr.
All rights reserved.