Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases

2017-07-07 02:10:07

The organization of web sites follows that of the book: data, tools, and useful tables. Each site's main page is listed, as are URLs for documentation (release notes, README files, etc.) and downloads.

C.1.1 Data Formats

C.1.1.1 DDBJ

Main site: http://www.ddbj.nig.ac.jp/
Release notes: http://www.ddbj.nig.ac.jp/ddbjnew/ddbj_relnote.html
Download: ftp://ftp.ddbj.nig.ac.jp/database/ddbj/

C.1.1.2 EMBL

Main page: http://www.ebi.ac.uk/embl/index.html
Release notes: http://www.ebi.ac.uk/embl/Documentation/Release_notes/current/relnotes.html
User manual: http://www.ebi.ac.uk/embl/Documentation/User_manual/usrman.html
Download: ftp://ftp.ebi.ac.uk/pub/databases/embl/

C.1.1.3 GenBank

GenBank overview: http://www.ncbi.nlm.nih.gov/Genbank/GenbankOverview.html
Release notes: ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt
Download: ftp://ftp.ncbi.nih.gov/genbank/
DDBJ/EMBL/GenBank Feature Table: http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html
NCBI Sequence Identifier Syntax: ftp://ftp.ncbi.nih.gov/blast/db/README
Non-redundant database: ftp://ftp.ncbi.nih.gov/blast/db/README

C.1.1.4 Pfam

Main page: http://pfam.wustl.edu/
Release notes: ftp://ftp.genetics.wustl.edu/pub/Pfam/relnotes.txt
Help pages: http://pfam.wustl.edu/help.shtml
Download: ftp://ftp.genetics.wustl.edu/pub/Pfam/

C.1.1.5 PROSITE

Main page: http://us.expasy.org/prosite/
Release notes: http://us.expasy.org/prosite/psrelnot.html
User manual: http://us.expasy.org/prosite/prosuser.html
Download: ftp://us.expasy.org/databases/prosite/

C.1.1.6 SWISS-PROT

Main page: http://us.expasy.org/sprot/
Release notes: http://us.expasy.org/sprot/relnotes/
User manual: http://us.expasy.org/sprot/userman.html
Download: ftp://us.expasy.org/databases/swiss-prot

C.1.2 Tools

C.1.2.1 BLAST

Main page: http://www.ncbi.nlm.nih.gov/BLAST/
Information guide: http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/information3.html
Download: ftp://ftp.ncbi.nih.gov/blast/executables/

C.1.2.2 BLAT

Main page: http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
User guide: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html
Download: http://www.soe.ucsc.edu/~kent/exe/

C.1.2.3 Clustal

Main page

http://www.ebi.ac.uk/clustalw/

User help

http://www.ebi.ac.uk/clustalw/clustalw_frame.html

Download

ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/

ftp://ftp.ebi.ac.uk/pub/software/dos/clustalw/

C.1.2.4 HMMER

Main page: http://hmmer.wustl.edu/
README: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/CURRENT/00README
Download: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.2g/hmmer-2.2g.tar.gz

C.1.2.5 EMBOSS

Main page: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/
User documentation: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/userdoc.html
Tutorial: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Doc/Tutorial/
Download: http://www.hgmp.mrc.ac.uk/Software/EMBOSS/download.html
Jemboss (Java API): http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Jemboss/

C.1.3 Common Tables

C.1.3.1 Nucleic Acids

Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (IUPAC IUBMB Joint Commission on Biochemical Nomenclature)

http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html

C.1.3.2 Genetic Codes

http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy/wprintgc?mode=t

C.1.3.3 Amino Acids

Nomenclature and Symbolism for Amino Acids and Peptides (IUPAC IUBMB Joint Commission on Biochemical Nomenclature)

http://www.chem.qmul.ac.uk/iupac/AminoAcid/

C.1.4 Miscellaneous

C.1.4.1 BioPerl

Main page: http://bioperl.org/
User documentation: http://bioperl.org/Core/Latest/modules.html
Mailing lists: http://bioperl.org/MailList.shtml
Download: http://bioperl.org/Core/Latest/index.shtml

C.1.4.2 BioJava

Main page

http://biojava.org/

User documentation

http://biojava.org/docs/started.html

http://biojava.org/docs/api/

Mailing lists

http://biojava.org/mailman/listinfo/biojava-l

http://biojava.org/mailman/listinfo/biojava-dev