Curr Protoc Bioinformatics. Author manuscript; available in PMC 2015 Mar 5.
PMCID: PMC4350995
Published in final edited form as:
NIHMSID: NIHMS257167
Curr Protoc Bioinformatics. 2010 Dec; 0 9: Unit–9.13.
PMID: 21154710
doi: 10.1002/0471250953.bi0913s32
Setting Up the JBrowse Genome Browser Mitchell E Skinner1 and Ian H Holmes 2 1 Institute for Quantitative Biosciences, UC Berkeley 2 Department of Bioengineering, UC Berkeley Contributed by Shonda A. Leonard (discussion of FASTA and GenBank file formats) Timothy G. Littlejohn (discussion of NCBI descriptor lines) IBM Life Sciences St. Leonards, NSW, Australia Andreas D. Baxevanis (discussion of PHYLIP, MSF, and NEXUS file formats) Bethesda, Maryland Copyright notice The publisher's final edited version of this article is available at Curr Protoc Bioinformatics See other articles in PMC that cite the published article.
Abstract
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INTRODUCTION
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BASIC PROTOCOL 1
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SETTING UP A JBROWSE INSTANCE USING FLATFILES AS A DATA SOURCE
Table 9.13.1
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Table 9.13.2
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Necessary Resources
$ cd $ bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa
$ bin/flatfile-to-json.pl --tracklabel gene --key “Gene” --gff docs/tutorial/data_files/volvox.gff3 --cssclass feature2 --getLabel --type gene --autocomplete all
Table 9.13.3
or
or
tracks
$ bin/flatfile-to-json.pl --bed docs/tutorial/data_files/volvox-remark.bed --tracklabel remark --key “Remark” -cssclass feature3 --getLabel --autocomplete label
$ bin/wig-to-json.pl --wig docs/tutorial/data_files/volvox_microarray.wig --tracklabel wiggle_example --key “20 degrees, 2 hr”
$ bin/generate-names.pl autocomplete
ALTERNATE PROTOCOL 1
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SETTING UP A JBROWSE INSTANCE USING A RELATIONAL DATABASE AS THE DATA SOURCE chado
Necessary Resources
$ mysql -u root mysql> create database jbrowse_example; Query OK, 1 row affected (0.00 sec) mysql> grant all on jbrowse_example.* to "@'localhost'; Query OK, 0 rows affected (0.00 sec)
$ bp_seqfeature_load.pl –dsn=dbi:mysql:jbrowse_example -adaptor=DBI::mysql --fast --create docs/tutorial/data_files/volvox.fa docs/tutorial/data_files/volvox.gff3
“db_args”: { “-adaptor”: “memory”, “-dir”: “docs/tutorial/data_files” },
“db_args”: { “-adaptor”: “DBI::mysql”, “-dsn”: “dbi:mysql:jbrowse_example” },
$ bin/prepare-refseqs.pl --conf docs/tutorial/conf_files/volvox.json --refs ctgA
$ bin/biodb-to-json.pl --conf docs/tutorial/conf_files/volvox.json
$ bin/generate-names.pl
ALTERNATE PROTOCOL 2
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SETTING UP A JBROWSE INSTANCE USING NCBI GENBANK FILES AS A DATA SOURCE
Necessary Resources
ftp://ftp.ncbi.nih.gov/genomes/Saccharomyces_cerevisiae/CHR_I/
$ bp_genbank2gff3.pl NC_001133.gbk
# sequence-region NC_001133 1 230208
##sequence-region NC_001133 1 230208
$ bin/prepare-refseqs.pl --conf docs/examples/config/yeast_genbank.json --refs NC_001133
$ bin/biodb-to-json.pl --conf docs/examples/config/yeast_genbank.json
$ bin/generate-names.pl
SUPPORT PROTOCOL 1
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DOWNLOADING/INSTALLING JBROWSE
Necessary Resources
$ sudo yum install perl
$ sudo apt-get install perl
$ sudo yum install gcc-c++ make libpng libpng-devel
$ sudo apt-get install g++ make libpng12-0 libpng12-dev
$ sudo cpan cpan> install CJFIELDS/BioPerl-1.6.1.tar.gz JSON JSON::XS
$ sudo yum install mysql perl-DBD-MySQL
$ sudo apt-get install mysql-server libdbd-mysql-perl
$ wget
$ unzip jbrowse*.zip
$ cd jbrowse* $ ./configure $ make
$ cd jbrowse* $ ./configure $ make GCC_LIB_ARGS=-L/usr/X11R6/lib GCC_INC_ARGS=-I/usr/X11R6/include
$ cd .. $ sudo mv jbrowse*/ /var/www/html/jbrowse
$ cd .. $ sudo mv jbrowse*/ /var/www/jbrowse
$ cd .. $ sudo mv jbrowse*/ /Library/WebServer/Documents/jbrowse
GUIDELINES FOR UNDERSTANDING RESULTS
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COMMENTARY
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Background Information
Critical Parameters and Troubleshooting
$ chmod −R o+r .
Acknowledgements
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APPENDIX 1B
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Common File Formats FASTA FILES
NCBI Descriptor Lines >gi|532319|pir|TVFV2E|TVFV2E envelope protein
Figure A.1B.1
Table A.1B.1
gb|accession|locus emb|accession|locus dbj|accession|locus pir||entry prf||name sp|accession|entry name pdb|entry|chain pat|country|number bbs|number gnl|database|identifier ref|accession|locus lcl|identifier
532319
gi
TVFV2E
TVFV2E envelope protein
gnl|PID|e1632 e
e1632
GenBank FLAT FILES
LOCUS ORIGIN
Table A.1B.2
LOCUS
PRI
ROD
MAM
VRT INV BCT SYN
PLN
VRL UNA
PHG EST
PAT
STS
GSS
HTC
DEFINITION
ACCESSION
PHYLIP FILES
VERSION
Figure A.1B.2
KEYWORDS
SOURCE
ORGANISM
REFERENCE
AUTHORS TITLE JOURNAL MEDLINE
FEATURES
FEATURE source
gene promoter TATA signal 5¢ UTR, 3¢ UTR .phy
CDS
MSF FILES
BASE COUNT
PileUp, !!NA MULTIPLE ALIGNMENT
!!AA MULTIPLE
ALIGNMENT ORIGIN P ORIGIN
ORIGIN
Figure A.1B.3
Figure A.1B.4
NEXUS FILES
#NEXUS DIMENSIONS
NTAX=5
NCHAR=547 MATRIX END; .nex
.nxs
Figure A.1B.5
CONVERTING BETWEEN FILE FORMATS
Footnotes
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This article describes in detail how JBrowse works and why. Internet Resources http://jbrowse.org/ The main JBrowse web site; has links to the JBrowse code, documentation, email lists, publications, and other internet resources relevant to JBrowse. DISCLAIMER This component of this unit by Dr. Andreas D. Baxevanis was written in his private capacity. No official support or endorsement by the National Institutes of Health or the United States Department of Health and Human Services is intended or should be inferred. INTERNET RESOURCES http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi ReadSeq biosequence interconversion tool. http://www.ebi.ac.uk/clustalw ClustalW multiple sequence alignment interface.
Literature Cited
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Key Reference
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