List of Biopython Packages For Bioinformatics
Biopython provides a comprehensive set of modules and packages that cover a wide range of functionalities in bioinformatics. Here is a list of some key Biopython modules/packages along with a brief description of their main functionalities:
1. Bio.Seq: Deals with biological sequences (DNA, RNA, and
proteins) and provides methods for manipulation, transcription, translation,
and more.
2. Bio.SeqIO: Handles reading and writing different sequence
file formats, such as FASTA, GenBank, and more.
3. Bio.Alphabet: Defines biological alphabets, like DNA,
RNA, and protein alphabets.
4. Bio.Align: Supports sequence alignment, including classes
for pairwise and multiple sequence alignments.
5. Bio.PDB: Works with protein structures and provides tools
for parsing and manipulating Protein Data Bank (PDB) files.
6. Bio.Entrez: Interacts with the NCBI Entrez databases,
allowing you to search and retrieve biological data.
7. Bio.Blast: Interacts with NCBI BLAST for performing
sequence similarity searches.
8. Bio.KEGG: Provides tools for accessing KEGG (Kyoto
Encyclopedia of Genes and Genomes) databases.
9. Bio.Cluster: Implements hierarchical and k-means
clustering algorithms for analyzing biological data.
10. Bio.Graphics: Generates graphical representations of
biological data, such as sequence annotations and phylogenetic trees.
11. Bio.PopGen: Analyzes population genetics data.
12. Bio.Statistics: Provides statistical tools for analyzing
biological data.
13. Bio.Motif: Deals with sequence motifs and motif
analysis.
14. Bio.Restriction: Handles information about restriction
enzymes and their recognition sites.
15. Bio.Nexus: Works with NEXUS format files commonly used
in phylogenetic analyses.
16. Bio.ExPASy: Interacts with the ExPASy server for
accessing bioinformatics tools and resources.
17. Bio.CodonUsage: Analyzes codon usage tables.
18. Bio.Medline: Deals with Medline and PubMed data for
literature searches.
19. Bio.GA: Implements genetic algorithms for optimization
problems in bioinformatics.
20. Bio.Phylo: Supports the manipulation and visualization
of phylogenetic trees.
21. Bio.Align.Applications: Allows you to run external
alignment tools (e.g., ClustalW, MUSCLE) from within Python scripts.
22. Bio.BioSQL: Provides a bridge between Biopython and the
BioSQL relational database schema, allowing you to store and retrieve
biological data.
23. Bio.SearchIO: Parses and works with various sequence
search output formats, such as BLAST and HMMER.
24. Bio.ExPASy.Scrape: Scrapes data from the ExPASy website,
including information on protein features and annotations.
25. Bio.pairwise2: Performs pairwise sequence alignments
with various algorithms and allows customization of the scoring system.
26. Bio.SeqUtils: Contains utility functions for analyzing
biological sequences, including GC content calculation, molecular weight, and
codon usage.
27. Bio.Align.Applications: Provides classes to work with
command-line tools for sequence alignment, such as ClustalW and MUSCLE.
28. Bio.Cluster: Implements clustering algorithms for
analyzing gene expression data.
29. Bio.KEGG.REST: Allows programmatic access to KEGG (Kyoto
Encyclopedia of Genes and Genomes) data through its RESTful web service.
30. Bio.GenBank: Handles GenBank files, allowing you to
extract information about genes, features, and annotations.
31. Bio.Medline.Record: Represents Medline records and
provides methods for parsing and manipulating Medline data.
32. Bio.ExPASy.Prodoc: Retrieves and parses information from
the Prosite documentation maintained by ExPASy.
33. Bio.Emboss: Provides interfaces to EMBOSS (European
Molecular Biology Open Software Suite) command-line tools.
34. Bio.Restriction.Analysis: Performs restriction enzyme
analysis on DNA sequences.
35. Bio.HMM: Implements Hidden Markov Models for sequence
analysis.
36. Bio.Graphics.GenomeDiagram: Generates customizable,
publication-quality diagrams of genomic features.
37. Bio.Cluster: Implements clustering algorithms for
analyzing gene expression data.
38. Bio.SubsMat: Handles substitution matrices commonly used
in sequence alignment.
39. Bio.SwissProt: Parses Swiss-Prot files, providing access
to protein information.
40. Bio.AlignIO.PharphyleticTree: Reads and writes files in
the Phylip/Newick tree format.
41. Bio.Align.AlignInfo: Provides tools for analyzing
information from sequence alignments, including consensus sequences and
conservation scores.
42. Bio.AlignIO.MafIO: Handles Multiple Alignment Format
(MAF) files commonly used in comparative genomics.
43. Bio.Compass: Implements a framework for pairwise
sequence comparison.
44. Bio.Data.CodonTable: Contains information about the
standard genetic code and several variant genetic codes used in different
organisms.
45. Bio.File: A collection of generic file handling
functions used across Biopython modules.
46. Bio.GA: Implements genetic algorithms for optimization
problems, often applied in bioinformatics.
47. Bio.Graphics.ColorSpiral: Generates color gradients for
use in graphical visualizations.
48. Bio.Graphics.Histogram: Creates histograms for sequence
data analysis.
49. Bio.Graphics.PhyloXML: Allows the creation of PhyloXML
format files for visualizing phylogenetic trees.
50. Bio.InterPro: Provides access to InterProScan results,
which predict protein families and domains.
51. Bio.MEME: Interfaces with the MEME suite for motif
discovery in biological sequences.
52. Bio.Mindy: Performs molecular dynamics simulations for
structural biology.
53. Bio.Motif.PWM: Represents Position Weight Matrices
commonly used in motif analysis.
54. Bio.Motif.Thresholds: Determines significance thresholds
for motif analysis results.
55. Bio.Phylo.PAML: Interfaces with the PAML (Phylogenetic
Analysis by Maximum Likelihood) software for evolutionary analysis.
56. Bio.SearchIO.hmmer3: Parses HMMER3 results files.
57. Bio.SeqUtils.ProtParam: Calculates various physical and
chemical properties of proteins.
58. Bio.SubsMat.MatrixInfo: Contains predefined substitution
matrices commonly used in sequence alignments.
59. Bio.Wise: Interfaces with the Wise2 package for DNA
sequence comparison.
60. Bio.SeqUtils.CodonUsage: Analyzes codon usage tables for
a given genetic code.