文件名称:
CSHL_Bioperl_I&&II.pdf
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文件大小: 38mb
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上传时间: 2019-08-17
详细说明：Topics to cover
•Introduction to BioPerl
•Using Sequence & Feature modules
•Using the modules for BLAST parser
•Accessing sequence databases
•Using the GFF processing modules
•GFF Database
•Evolutionary data
•Trees and Population data
Overview of Toolkit
•Bioperl is...
•A Set of Perl modules for manOverview of toolkit
o Bioperl iS
■■■
A Set of Perl modules for manipulating
genomic and other biological data
An Open Source Toolkit with many
contributors
a flexible and extensible system for
doing bioinformatics data manipulation
Some things you can do
Read in sequence data from a file in standard
formats ASTA, GenBank, EMBL, SwissProt, .
e Manipulate sequences, reverse complement
translate coding DNA sequence to protein
Parse a BLAST report, get access to every bit of
data in the report
Major Areas covered in Bioperl
e Sequences, Features, Annotations
Pairwise alignment reports
Multiple Sequence Alignments
● Bibliographic data
Graphical Rendering of sequence tracks
Database for features and sequences
Additional things
Gene prediction parsers
Trees, Parsing Phylogenetic and
Molecular Evolution software output
Population genetic data and summary
statistics
● Taxonomy
Protein structure
Practical Examples
Manipulate a dna or Protein Sequence
Read and write different Sequence formats
o Extract sequence annotations and features
Parse a BLAST report
How the code is organized
http://cvs.oPen-bio.org
e bioperl-live- Core packages
bioperl-run-for running applications
bioperl-ext -C language extension
bioperl-db-bioperl BiosQL implementation
bioperl-pedigree, bioperl-microarray are side
projects
Within bioperl-live( core
Bio/ top-level
Bio Seqlo -sequence input/output
Bio: PrimarySeq pm basic sequence obj
o Bio: SearchlO-parsers for BLAST, FASTA
Bio AlignlO-multiple sequence alignments
Bio: Tools-misc collection of parsers for different
programs
Website
.http://bioperl.orgorhttp://bio.perlorg
Wiki based documentation
Project Tracking
HOWTOS
Frequently Asked Questions( FAQ)
News
Links to online documentation
http:/bugzilla.open-bio.org-bugtracking
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