USEFUL INTERNET SITES:
(European Molecular Biology Open Software Suite) is a suite of free
software tools for sequence analysis. There are a wide variety of
programs that make up the suite, ranging in application from database
searching to presentation of sequence data.
The University of Saskatchewan maintains a portal to a graphical user interphase to Emboss - Haruspex
In Roman and Etruscan times a haruspex was a man trained to fortell the
future by inspecting the entrails of sacrificed animals!
2. EMBL Bioinformatics:
A software directory of general interest in molecular biology and genetics.
3. National Center for Biotechnology Information (NCBI):
in 1988 as an international resource for molecular biology information,
NCBI creates public databases, conducts research in computational
biology, develops software tools for analyzing genome data, and
disseminates biomedical information - all for the better understanding
of molecular processes affecting human health and disease.
4. ExPASy Molecular Biology Server:
ExPASy (Expert Protein Analysis System) proteomics server of the Swiss
Institute of Bioinformatics (SIB) is dedicated to the analysis of
protein sequences and structures as well as 2-D PAGE
5. National human genome research institute, genomic and genetic resources on the WWW :
6. Molecular Biology Protocols:
Catalogue of books on molecular biology protocols
Tools for prediction and analysis of protein coding gene structure.
8. Martindale’s Calculators Online Center:
Over twenty thousand calculators for almost every conceivable use.
9. New England BioLabs, technical reference:
Gateway to NCBI nucleotide (Genbank), protein, journal (Pubmed), databases
2. The human genome:
3. The mouse genome:
4. The rat genome:
5. Dog genome resources:
6. Bovine genome resources:
also see http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9913
7. Horse genome resources:
8. Myotis lucifugus genome (not annotated, but allows search of homologues using BLAST)
9. Saccharomyces genome database:
is a scientific database of the molecular biology and genetics of the
yeast Saccharomyces cerevisiae, which is commonly known as baker's or
10. Chaperonin database:
11. Ribosomal database project:
12. Viral Bioinformatics Resource Centre:
C. Sequence alignment tools:
1. NCBI BLAST:
3. Clustal W reference information:
D. Other useful tools:
1. GENSCAN webserver:
server provides access to the program Genscan for predicting the
locations and exon-intron structures of genes in genomic sequences from
a variety of organisms.
2. ORF finder:
3. The PREDICTPROTEIN server:
is a service for sequence analysis, and structure prediction. You
submit any protein sequence. PredictProtein retrieves similar sequences
in the database and predicts aspects of protein structure.
Examines proteins for potential trans-membrane domains
Prediction of protein sorting signals and localization sites in amino acid sequences
is a database of protein families and domains. It consists of
biologically significant sites, patterns and profiles that help to
reliably identify to which known protein family (if any) a new sequence
8. Peptide mass calculator:
[references] cleaves a protein sequence from the SWISS-PROT and/or
TrEMBL databases or a user-entered protein sequence with a chosen
enzyme, and computes the masses of the generated peptides. The tool
also returns theoretical isoelectric point and mass values for the
protein of interest. If desired, PeptideMass can return the mass of
peptides known to carry posttranslational modifications, and can
highlight peptides whose masses may be affected by database conflicts,
isoforms or splicing variants.
9. Compute pI/Mw tool:
pI/Mw is a tool which allows the computation of the theoretical pI
(isoelectric point) and Mw (molecular weight) for a list of SWISS-PROT
and/or TrEMBL entries or for a user entered sequence
10. Restriction enzyme analysis:
REMAP at Mobyle:
RESTRICT at Mobyle:
11. Invitrogen’s OligoPerfect Designer:
12. Sequence scanner (Applied Biosystems) – a Windows program that allows you to see sequence traces from sequencing runs.
13. siRNA software:
Ambion RNA interference resource:
Software for filtering ineffective siRNAs and improving siRNA design (Bioinformatics 2005, 21:144-151):
E. 3 D viewers:
RasMol is a program for molecular graphics visualization originally developed by Roger Sayle.