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Molecular
Genetics
Resources
- Major Bioinfomatics Sites
- UTHSCSA resources:
- Bo Demeler's
Bioinformatics
page. (locally supported programs)
- General
documentation
(General connections, ssh, webmail).
- Genomics
(DNA star, Vector NTI, Oligo, GCG, Emboss & mse, Phred/phrap,
Hmmer,
Phylip, Topo, SAM).
- Structure
(Insight II, Modeler, Shake and Bake, Hydro).
- Local blast
(web
interface
to blast on local mirror of ncbi databases - this will work during
periods
when ncbi bogs down. You need your username and password
corresponding
to a bcf account).
- Ultrascan.
- Database
engines (Oracle, MySQL).
- Obtaining
accounts.
- Sites devoted to organisms:
- Harvard Dept. of
Mol. Cell.
Biology.
- Biosci/bionet.
- Molecular Evolution:
- Sites related to repetitive sequences
- REBASE. a database of
restriction
enzymes.
- Restriction enzyme
site search,
Webcutter.
- Restriction
enzyme
site
search.
- Complement
a
sequence
at a web site.
- Genome Centers:
- Genetic Maps
- microRNA
- Protein structure resources:
- Protein families:
- TIGRFAMs
- HHPred
- PROSITE
(http://expasy.cbr.nrc.ca/prosite/)
(http://ca.expasy.org/prosite/) - curated motif-defined familes, and
some
profiles.
- SBASE
Protein
families
by nonseeded cluster analysis (http://hydra.icgeb.trieste.it/sbase/).
- PRODOM
- PSI-blast results seeded with Pfam.
(http://protein.toulouse.inra.fr/prodom.html).
- Pfam - Curated profiles, extended sets from searching with the
profiles,
and other domains from PRODOM.
- Blocks - Automatically
constructed
motifs from the various protein family databases.
- ProtoMap
(http://protomap.stanford.edu/)
- hierarchical clustering of all sequences in SwissProt.
- SMART
(http://smart.embl-heidelberg.de/)
- profiles from curated alignments of signaling domains.
- PRINTS
(http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/)
- groups motifs together into a fingerprint which is used to search for
a domain or family.
- Interpro
(http://www.ebi.ac.uk/interpro/)
- a database that collates information from Pfam, PRINTS, PROSITE,
ProDom,
SMART, and the SWISS-PROT + TrEMBL protein databases.
- [Gone ?] Molecular Information
Agent
(http://mia.sdsc.edu/).
It launches a mass search against about 50 databases. An
accession
number for Swiss Prot or PDB is probably the best search key for it,
but
NCBI accession numbers, keywords, or even sequence is accepted as a
search
key. Also, they have an excellent list of web sites for relevant
databases.
- Protein multiple alignment:
- Weblogo (http://weblogo.berkeley.edu/).
Procaryotic
promoter prediction.
(http://www.fruitfly.org/seq_tools/promoter.html).
- tRNAscan-SE
(http://lowelab.ucsc.edu/tRNAscan-SE/)
- Coils
server
at EMBnet (http://www.ch.embnet.org/software/COILS_form.html) for
coiled
coil prediction from sequence.
- SAM
- Sequence
Alignment and Modeling tool.
(http://www.cse.ucsc.edu/research/compbio/sam.html)
- Hidden Markov Models applied to alignment and family definition.
- Parent site is the UCSC
Computational
Biology Group (http://www.cse.ucsc.edu/research/compbio/).
- Psipred
(http://bioinf.cs.ucl.ac.uk/psipred/)
- secondary structure prediction from sequence alone.
- Prof
Liao's
Bioinformatics
Group. (Dr. Li Liao, Univ. of Deleware)
Servers: TMMOD (transmembrane topology), CASA (Alignment accuracy),
QC-COMP
(comparison of HMMs).
- TMHMM.
(http://www.cbs.dtu.dk/services/TMHMM-2.0/).
Transmembrane helix prediction.
- Consurf
(http://consurf.tau.ac.il/)
- Server for the Identification of Functional Regions in Proteins by
Surface-Mapping
of Phylogenetic Information.
- NIH Center for
Molecular Modeling
(http://cmm.info.nih.gov/modeling). - Particularly note index of
tutorials
for modeling programs.
- Codon usage database.
- GeneMark
(http://opal.biology.gatech.edu/GeneMark/).
- BioBase -
(http://www.gene-regulation.com/).
- Has taken over TRANSFAC, a database of transcription factor
binding
sites
and various programs for using the database. Free for academic use, but
also there is a "professional" version for a fee.
- Regulatory Sequence
Analysis
tools.
- A selection of free bioinformatics tools provided by genscript.com.
- Stastical
Analysis
of
Protein Sequence (SAP)
(http://www.isrec.isb-sib.ch/software/SAPS_form.html).
- MyHits
-
An interface
to a variety of protein domain databases that includes some capacity
for
a private workspace and includes both motif scanning and profile
scanning.
- GRAIL - neural network for prediction of coding sequences, taking
account
of p(A) sites, repetitive sequences, and CpG islands.
- Parent site: Computational
Biology
at
Oak Ridge National Laboratory (http://compbio.ornl.gov/) - at the
last
inspection of this site it appears to have become dated. The help
manual
is off line.
- Grail search page
(http://compbio.ornl.gov/Grail-1.3/).
- At the parent site, see also:
- GrailEXP - Grail supplemented with EST searching. Also
attempts
to
predict alternative splicing.
- Genome catalogue and genome channel - genome browsers.
- Pipeline - Grail coupled to blast search annotation.
- Domain Parser - diagnoses domains in a PDB entry by residue
proximity.
- PROSPECT - a threader including position-specific score
matrixes,
secondary
structure fitting, contact potentials, and alignment gap penalties.
- EmbNet.
- Downloadable
dotplotter See ~/apps/dotter.d in bcf, or \Programs in VISTA
laptop. See also dotmatcher in EMBOSS package. tfm dotmatcher on bcf.
- Biotoolkit
-
An
index to many online resources..
- UCSC
Computational Biology
- Includes access to SAM.
- Staden Seq.
Assembly
Programs.
- Phred/Phrap.
- PDraw
(http://www.acaclone.com).
- Freeware for drawing plasmids, primer design, and restriction mapping.
- Primer3 - PCR primer
picking
program
at MIT.
- Microarray
Construction
guide.
- VISTA (genomic
sequence
and
annotation alignment package) (http://www-gsd.lbl.gov/vista/)
- Bioinformatics
tutorials
at
IMIM. (http://genome.imim.es/main/seminars.html#SEM)
- Indexes to useful links:
- ATCC (http://www.atcc.org/)
-
Repository
of strains of all kinds.
- Dave Lapointe's web server: (biotools.umassmed.edu).
- BioGrid ( http://biogrid.uta.edu/
). - A UT Arlington supercomputing initiative.
- Experimental protocols:
- Beginner's
Guide
to Molecular Biology.
- Microbiology Information
(http://www.microbes.info/).
- Sites with downloadable genome annotation GUIs
- Genomorama
(http://public.lanl.gov/jgans/genomorama/)
- GBROWSE
(http://www.gmod.org/?q=node/71).
- Software related to displaying or simulating biological or
regulatory
networks.
- Sites related to microarray data and related expression studies:
- Sites related to mass spectrometry, or statistics in support.
Journals
(Instructions
to Authors)
Computer How
To...
Misc. Bookmarks:
Other Labs
Search engines
Companies
UTHSCSA links.
Disclaimer: No endorsements are implied and no advertising fees
have been paid. This is simply a list of links that I had some
reason
or other to want to remember. I have no editorial influence over
any page unless it is subordinate to
http://biochem.uthscsa.edu/~hs_lab/,
or http://www.bioinformatics.uthscsa.edu/, or
http://dentalbioc.uthscsa.edu/
- S.C. Hardies
Last major update: 5/20/11
Last addition 2-11-12
Stephen
C. Hardies home page.
Web page maintained by Stephen C. Hardies, Department of Biochemistry,
University of Texas Health Science Center at San Antonio