MARC: Developing Bioinformatics Programs Alex Ropelewski PSC-NRBSC Bienvenido Vélez UPR Mayaguez Essential BioPython: Overview 1

What is BioPython? 2  An Open Source Python module that provides many functions that are highly relevant to bioinformatics:  Functions to read sequences in a variety of file formats  Functions to query databases over the network  Functions to parse output from sequence analysis programs  Functions to perform sequence analysis  BioPython website contains the BioPython module plus tutorials and examples: 

 Affy Affy  Align Align  AlignIO AlignIO  Alphabet Alphabet  Application Application  Blast Blast  CAPS CAPS  Cluster Cluster  Compass Compass  Crystal Crystal  Data Data  DocSQL DocSQL  Emboss Emboss  Entrez Entrez  ExPASy ExPASy  FSSP FSSP  File File  GA GA  GenBank GenBank  Geo Geo  Graphics Graphics  HMM HMM  HotRand HotRand  Index Index  KDTree KDTree  KEGG KEGG  LogisticRegression LogisticRegression  MarkovModel MarkovModel  MaxEntropy MaxEntropy  Medline Medline  Motif Motif  NMR NMR  NaiveBayes NaiveBayes  NeuralNetwork NeuralNetwork  Nexus Nexus  PDB PDB  ParserSupport ParserSupport  Pathway Pathway  Phylo Phylo  PopGen PopGen  Restriction Restriction  SCOP SCOP  SVDSuperimposer SVDSuperimposer  Search Search  SearchIO SearchIO  Seq Seq  SeqFeature SeqFeature  SeqIO SeqIO  SeqRecord SeqRecord  SeqUtils SeqUtils  Sequencing Sequencing  Statistics Statistics  SubsMat SubsMat  SwissProt SwissProt  TogoWS TogoWS  UniGene UniGene  UniProt UniProt  Wise Wise  _py3k _py3k  _utils _utils  bgzf bgzf  kNN kNN  motifs motifs  pairwise2 pairwise2  Stringfns Stringfns  Triefind Triefind Essential BioPython Modules 3

 Affy Affy  Align Align  AlignIO AlignIO  Alphabet Alphabet  Application Application  Blast Blast  CAPS CAPS  Cluster Cluster  Compass Compass  Crystal Crystal  Data Data  DocSQL DocSQL  Emboss Emboss  Entrez Entrez  ExPASy ExPASy  FSSP FSSP  File File  GA GA  GenBank GenBank  Geo Geo  Graphics Graphics  HMM HMM  HotRand HotRand  Index Index  KDTree KDTree  KEGG KEGG  LogisticRegression LogisticRegression  MarkovModel MarkovModel  MaxEntropy MaxEntropy  Medline Medline  Motif Motif  NMR NMR  NaiveBayes NaiveBayes  NeuralNetwork NeuralNetwork  Nexus Nexus  PDB PDB  ParserSupport ParserSupport  Pathway Pathway  Phylo Phylo  PopGen PopGen  Restriction Restriction  SCOP SCOP  SVDSuperimposer SVDSuperimposer  Search Search  SearchIO SearchIO  Seq Seq  SeqFeature SeqFeature  SeqIO SeqIO  SeqRecord SeqRecord  SeqUtils SeqUtils  Sequencing Sequencing  Statistics Statistics  SubsMat SubsMat  SwissProt SwissProt  TogoWS TogoWS  UniGene UniGene  UniProt UniProt  Wise Wise  _py3k _py3k  _utils _utils  bgzf bgzf  kNN kNN  motifs motifs  pairwise2 pairwise2  Stringfns Stringfns  Triefind Triefind Essential BioPython Modules 4

BioPython Modules Discussed 5 ModuleDescription Seq Provides Tools to Represent DNA and Protein Sequences and Operations on these Sequences SeqRecord Provides Tools to Represent DNA and Protein Records Including Metadata and Annotations SeqIO Provides Methods to Extract (Parse) Information from Sequence Files in Multiple Formats (e.g. FASTA, XML) Entrez UniProt Provides Methods to Retrieve DNA/Protein Sequence Files from the Entrez or UniProt Online Databases Blast Provides Methods to Perform BLAST searches over the network and analyze their results

 Use your own routine when:  The algorithm or coding is interesting to you  BioPython data structure mapping is too complex for your task  You want to “own” the source code from a copyright perspective  Use Biopython when:  Routine fits your needs  Routine is unchallenging or boring - Why waste your time?  Routine will take you a lot of effort to write  Extend Biopython routine when:  Routine almost does what you want but not quite  Challenging for the beginning programmer! Can you read and understand someone else’s code? BioPython vs Your Own Routines 6

Essential BioPython Road Map 7 Install Mac Install Mac Install PC Install PC Sequence Objects Sequence Objects Manipulating Sequence Files Manipulating Sequence Files Retrieving Sequences from the Web Retrieving Sequences from the Web Searching Sequences Using BLAST Searching Sequences Using BLAST