Welcome to laboratory of Amit Pandey at University of Bern
Welcome to laboratory of Amit Pandey at University of Bern

Links for servers and software for Bioinformatics courses for students at University of Bern



UCSC Genome Browser          NCBI Map Viewer   


Yeast Genome    Microbial Genomes  

 FlyBase http://flybase.bio.indiana.edu/  

 WormBase http://www.wormbase.org 

 TAIR http://www.arabidopsis.org/

 Literature  PUBMED www.ncbi.nlm.nih.gov/pubmed    Science Citation Index

 OMIM http://www3.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM 

 BIND http://www.blueprint.org/bind/bind.php 

 GO http://www.geneontology.org/ 

 BLAST servers  NCBI  www.ncbi.nlm.nih.gov/blast              

 EBI  www.ebi.ac.uk/blast            

 EMBNet  www.expasy.ch/blast                      

 BLAT Search for Genomes BLAT

 Seq alignment  Blast2Seq    Lalign   TCoffee         ClustalW           

 Sequence conversion: ReadSeq

 Alignment Editors  GeneDoc  CINEMA  BOXSHADE  JALVIEW  CLC Sequence Viewer (Very good tool for local install)
 DNA Seq Analysis  BioTools  NEBcutter   Sequence Editor   Nucleic Acid Sequence Massager 

 Feature Extractor     ORF Finder   VectorScreen

 Prot Seq Analysis  ProtParam tool (Physical and Chemical Properties of a given Protein Sequence)

 Peptide Cutter (Digestion of Proteins)

 PIR http://pir.georgetown.edu/           MIPS http://mips.gsf.de/             

 UniProt http://www.uniprot.org/

 Protein family  PROSITE http://www.expasy.org/prosite/               

 PRINTS http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ 
 Blocks http://blocks.fhcrc.org/                                  

 Profiles http://hits.isb-sib.ch/cgi-bin/PFSCAN/ 
 Pfam http://www.sanger.ac.uk/Software/Pfam/      

 eMOTIF http://fold.stanford.edu/emotif/ 
 InterPro http://www.ebi.ac.uk/interpro/

 Protein structure  PDB http://www.rscb.org/pdb/ 
 SCOP http://scop.mrc-lmb.cam.ac.uk/scop/ 

 CATH http://www.biochem.ucl.ac.uk/bsm/cath/        

 PDBsum http://www.biochem.ucl.ac.uk/bsm/pdbsum/ 

 CDD http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml 

 3D Str Prediction  Swiss Model   HHPRED
 Metabolic/pathway  KEGG http://www.genome.ad.jp/          
 WIT http://www-wit.mcs.anl.gov/Gongxin/           
 EcoCyc http://ecocyc.org/  
 UMBBD http://umbbd.ahc.umn.edu/ 



PD Dr. Amit V Pandey
Pediatric Endocrinology, Diabetology and Metabolism,

KIKL C837, Inselspital

University Children's Hospital Bern,

Freiburgstrasse 15, 3010 Bern


Tel: +41 31 632 9637 (Office)

        +41 31 632 9527 (Lab)

E-mail: amit@pandeylab.org


Tweets from Amit V Pandey @Pandeylab


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