Amelaye's BioPHP demo

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.

Cloning (new in BioPHP 2.0)

Plasmid from GenBank pUC19 as a circular Plasmid: features, translation, overlaps, origin. Restriction digest Circular digest of pUC19, fragments, sticky ends and their compatibility. Gibson assembly Homology arms for an insert, and the junction check. GenBank, GFF3 and BED export Write the annotated plasmid in three formats.

Phylogenetics (new in BioPHP 2.0)

UPGMA tree A rooted tree of five bacteria from their 5S rRNA distances. Neighbor-Joining versus UPGMA When the molecular clock does not hold, only neighbor-joining finds the right tree. Newick format Read a tree of the great apes, write it back, and catch malformed trees.

Variants (new in BioPHP 2.0)

Read a VCF file The example of the VCF 4.3 specification: SNVs, indels, multi-allelic sites. Write a VCF file BRAF V600E and structural variants, written then read back unchanged. Variants in a database Store variants with Doctrine, then query them.