Vikram MisraIntroductionExercisesPrerequisitesScheduleGuest LecturesUseful Web sitesReferences
USEFUL INTERNET SITES:

A. General:

1.
EMBOSS (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): 
Established 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
The 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

7. Webgene:  
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

B. Databases:

1. Entrez
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
SGDTM is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.

10. Chaperonin database

11. Ribosomal database project

12. Viral Bioinformatics Resource Centre


C. Sequence alignment tools:

1. NCBI BLAST

3. Clustal W reference information

Download Clustal:

Mac: 1
 2 

PC



D. Other useful tools:

1. GENSCAN webserver
This 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: 
PredictProtein 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.

5. TmPred
Examines proteins for potential trans-membrane domains

6. PSORT
Prediction of protein sorting signals and localization sites in amino acid sequences

7. PROSITE
PROSITE 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 belongs.

8. Peptide mass calculator
PeptideMass [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
Compute 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:

Web Cutter:

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:

1. RasMol
RasMol is a program for molecular graphics visualization originally developed by Roger Sayle.