Amelaye's BioPHP demo

A modern PHP library for bioinformatics,
simple, powerful and extensible.

Code Samples

Discover BioPHP through concrete, ready-to-use examples.

Sequencing

Simple sequence analysis Sample code and result for a basic sequence analysis. FASTA alignement Read and parse a FASTA alignment. Clustal parsing CLUSTAL alignment: several examples, demo of all the functions. Play with sequencies The sequence as a value object (new in BioPHP 1.1). Play with proteins The protein as a value object (new in BioPHP 1.1). Sequence match Find matches inside a sequence. Restriction enzyme Name, pattern, cut position and length of restriction enzymes.

Database parsers

GENBANK Puts GENBANK into database and loads a array of objects. SWISSPROT Puts SWISSPROT into database and loads a array of objects. PRF Protein Research Foundation record. PIR Protein Information Resource record. UniGene EST cluster record. GENOME Whole-genome record. HGBASE Human genome variation record. PRINTS Protein fingerprint record. ProDom Protein domain family record. AAindex Amino acid index record. EPD Eukaryotic Promoter Database record.

BioTools

Browse a collection of integrated, ready-to-use bioinformatics tools.

Chaos Game Representation of DNA Graphical representation of genomes and oligonucleotide frequencies. FCGR Chaos Game Representation of DNA Graphical representation of genomes and oligonucleotide frequencies. CGR Distance among sequences Oligonucleotide frequency based comparison of composition. Stats DNA to protein translation Translate a DNA sequence into its protein sequence. DNA Palindromic sequences finder Locate palindromic motifs in a DNA sequence. DNA GC Content Finder Compute the GC content of an uploaded FASTA file. DNA Melting Temperature (Tm) Calculation Estimate the melting temperature of a DNA duplex. DNA Microarray Data Analysis Adaptive quantification method. Stats Microsatellite repeats finder Detect short tandem repeats in a sequence. DNA Frequency of nucleotides Nucleotide and oligonucleotide frequencies in a sequence. Stats PCR amplification In silico PCR amplification. DNA Protein sequence properties Protein sequence information and derived properties. Protein Protein to DNA reverse translation Reverse-translate a protein into a DNA sequence. Protein Random sequences Generate random DNA, RNA or protein sequences. Tools Reduced alphabets for proteins Redundant or simplified alphabets for proteins. Protein Restriction enzyme digest of DNA With commercially available restriction enzymes. DNA Sequence alignment Alignment of two DNA, RNA or protein sequences. Aligner DNA sequence manipulation Manipulate a DNA sequence and read its properties. DNA Skews generator GC-, AT-, KETO- and oligo-skews from custom sequences. Stats Formula functions Useful formulas for sequence and protein calculations. Tools