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BioPHP: PHP for Biocomputing

Last updated: May 12, 2003

Medium-length scripts

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Sequence Records Query-by-Example (QBE) Script

Script that searches for sequence records that meet certain criteria given by user in a QBE-like manner.

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 GenePHP 1.1.

Find a Pair of Restriction Sites in a Sequence

A tool that helps the user select a restriction enzyme with which to cut or extract a target fragment within a larger DNA sequence.

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.

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Short scripts

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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.