Biopython Tutorial and Cookbook - Biopython · Biopython

1 Biopython Tutorial and CookbookJeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck,Michiel de Hoon, Peter Cock, Tiago Antao, Eric Talevich, Bartek Wilczy nskiLast Update 25 May 2020 ( Biopython )Contents1 What is Biopython ? .. What can I find in the Biopython package .. Installing Biopython .. Frequently Asked Questions (FAQ) ..102 Quick Start What can you do with Biopython ? General overview of what Biopython provides .. Working with sequences .. A usage example .. Parsing sequence file formats .. FASTA parsing example .. GenBank parsing example .. love parsing please don t stop talking about it! .. Connecting with biological databases .. What to do next ..183 Sequence Sequences and Alphabets .. Sequences act like strings .. Slicing a sequence .. Turning Seq objects into strings .. Concatenating or adding sequences .. Changing case .. Nucleotide sequences and (reverse) complements.

2 Transcription .. Translation .. Translation Tables .. Comparing Seq objects .. MutableSeq objects .. UnknownSeq objects .. Working with strings directly ..334 Sequence annotation The SeqRecord object .. Creating a SeqRecord .. objects from scratch .. objects from FASTA files .. objects from GenBank files .. Feature, location and position objects .. objects .. and locations .. described by a feature or location .. Comparison .. References .. The format method .. Slicing a SeqRecord .. Adding SeqRecord objects .. Reverse-complementing SeqRecord objects ..495 Sequence Parsing or Reading Sequences .. Sequence Files .. over the records in a sequence file .. a list of the records in a sequence file .. data .. data .. Parsing sequences from compressed files .. Parsing sequences from the net .. GenBank records from the net .. SwissProt sequences from the net .. Sequence files as Dictionaries.

3 Files as Dictionaries In memory .. files as Dictionaries Indexed files .. files as Dictionaries Database indexed files .. compressed files .. Writing Sequence Files .. trips .. between sequence file formats .. a file of sequences to their reverse complements .. your SeqRecord objects as formatted strings .. Low level FASTA and FASTQ parsers ..706 Multiple Sequence Alignment Parsing or Reading Sequence Alignments .. Alignments .. Alignments .. Alignments .. Writing Alignments .. between sequence alignment file formats .. your alignment objects as formatted strings .. Manipulating Alignments .. alignments .. as arrays .. Alignment Tools .. using stdout .. using stdin and stdout .. needle and water .. Pairwise sequence alignment .. Substitution matrices .. 1127 Running BLAST over the Internet .. Running BLAST locally .. NCBI BLAST+ .. versions of BLAST .. Parsing BLAST output.

4 The BLAST record class .. Dealing with PSI-BLAST .. Dealing with RPS-BLAST .. 1268 BLAST and other sequence search The SearchIO object model .. A note about standards and conventions .. Reading search output files .. Dealing with large search output files with indexing .. Writing and converting search output files .. 1449 Accessing NCBI s Entrez Entrez Guidelines .. EInfo: Obtaining information about the Entrez databases .. ESearch: Searching the Entrez databases .. EPost: Uploading a list of identifiers .. ESummary: Retrieving summaries from primary IDs .. EFetch: Downloading full records from Entrez .. ELink: Searching for related items in NCBI Entrez .. EGQuery: Global Query - counts for search terms .. ESpell: Obtaining spelling suggestions .. Parsing huge Entrez XML files .. HTML escape characters .. Handling errors .. Specialized parsers.

5 Parsing Medline records .. Parsing GEO records .. Parsing UniGene records .. Using a proxy .. Examples .. PubMed and Medline .. Searching, downloading, and parsing Entrez Nucleotide records .. Searching, downloading, and parsing GenBank records .. Finding the lineage of an organism .. Using the history and WebEnv .. Searching for and downloading sequences using the history .. Searching for and downloading abstracts using the history .. Searching for citations .. 17310 Swiss-Prot and Parsing Swiss-Prot files .. Parsing Swiss-Prot records .. Parsing the Swiss-Prot keyword and category list .. Parsing Prosite records .. Parsing Prosite documentation records .. Parsing Enzyme records .. Accessing the ExPASy server .. Retrieving a Swiss-Prot record .. Searching Swiss-Prot .. Retrieving Prosite and Prosite documentation records .. Scanning the Prosite database.

6 18211 Going 3D: The PDB Reading and writing crystal structure files .. Reading an mmCIF file .. Reading files in the MMTF format .. Reading a PDB file .. Reading a PQR file .. Reading files in the PDB XML format .. Writing mmCIF files .. Writing PDB files .. Writing PQR files .. Writing MMTF files .. Structure representation .. Structure .. Model .. Chain .. Residue .. Atom .. Extracting a specificAtom/Residue/Chain/Modelfrom a Structure .. Disorder .. General approach .. Disordered atoms .. Disordered residues .. Hetero residues .. Associated problems .. Water residues .. Other hetero residues .. Navigating through a Structure object .. Analyzing structures .. Measuring distances .. Measuring angles .. Measuring torsion angles .. Internal coordinates for standard residues .. Determining atom-atom contacts .. Superimposing two structures.

7 Mapping the residues of two related structures onto each other .. Calculating the Half Sphere Exposure .. Determining the secondary structure .. Calculating the residue depth .. Common problems in PDB files .. Examples .. Automatic correction .. Fatal errors .. Accessing the Protein Data Bank .. Downloading structures from the Protein Data Bank .. Downloading the entire PDB .. Keeping a local copy of the PDB up to date .. General questions .. How well tested is .. How fast is it? .. Is there support for molecular graphics? .. Who s using .. 20512 : Population GenePop .. 20613 Phylogenetics with Demo: What s in a Tree? .. Coloring branches within a tree .. I/O functions .. View and export trees .. Using Tree and Clade objects .. Search and traversal methods .. Information methods .. Modification methods .. Features of PhyloXML trees.

8 Running external applications .. PAML integration .. Future plans .. 21814 Sequence motif analysis using Motif objects .. Creating a motif from instances .. Creating a sequence logo .. Reading motifs .. JASPAR .. MEME .. TRANSFAC .. Writing motifs .. Position-Weight Matrices .. Position-Specific Scoring Matrices .. Searching for instances .. Searching for exact matches .. Searching for matches using the PSSM score .. Selecting a score threshold .. Each motif object has an associated Position-Specific Scoring Matrix .. Comparing motifs .. novomotif finding .. MEME .. links .. 246515 Cluster Distance functions .. Calculating cluster properties .. Partitioning algorithms .. Hierarchical clustering .. Self-Organizing Maps .. Principal Component Analysis .. Handling Cluster/TreeView-type files .. Example calculation .. 26816 Supervised learning The Logistic Regression Model.

9 Background and Purpose .. Training the logistic regression model .. Using the logistic regression model for classification .. Logistic Regression, Linear Discriminant Analysis, and Support Vector Machines .. Neighbors .. Background and purpose .. Initializing ak-nearest neighbors model .. Using ak-nearest neighbors model for classification .. Na ve Bayes .. Maximum Entropy .. Markov Models .. 27817 Graphics including GenomeDiagram .. Introduction .. Diagrams, tracks, feature-sets and features .. A top down example .. A bottom up example .. Features without a SeqFeature .. Feature captions .. Feature sigils .. Arrow sigils .. A nice example .. Multiple tracks .. Cross-Links between tracks .. Further options .. Converting old code .. Chromosomes .. Simple Chromosomes .. Annotated Chromosomes .. 30318 Parsing KEGG records.

10 Querying the KEGG API .. 30519 : analyse phenotypic Phenotype Microarrays .. Parsing Phenotype Microarray data .. Manipulating Phenotype Microarray data .. Writing Phenotype Microarray data .. 312620 Cookbook Cool things to do with Working with sequence files .. Filtering a sequence file .. Producing randomised genomes .. Translating a FASTA file of CDS entries .. Making the sequences in a FASTA file upper case .. Sorting a sequence file .. Simple quality filtering for FASTQ files .. Trimming off primer sequences .. Trimming off adaptor sequences .. Converting FASTQ files .. Converting FASTA and QUAL files into FASTQ files .. Indexing a FASTQ file .. Converting SFF files .. Identifying open reading frames .. Sequence parsing plus simple plots .. Histogram of sequence lengths .. Plot of sequence GC% .. Nucleotide dot plots .. Plotting the quality scores of sequencing read data.