Guide: Helps you in sequence analysis. The model experiment is divided into ten steps which includes 1) Sequence retrieval (Pubmed, Genbank, SwissProt, Readseq), 2) ORF prediction and translation (Genefinder, Genscan, Grail, translation tool), 3) Sequence similarity search (BLAST & FASTA) 4) Global alignment (Bayes Block aligner, BCM Pairwise aligner) 5) Multiple sequence  alignment(ClustalW, Blocks and Macaw). 6) Pattern search (PFScan, Motif finder, Pfam, Prosite) 7) Finding sequences from other species 8) Protein Structure Prediction (PDB Blast, JPRED, Threader2, 3DPSSM, Coils, MODELLER and Swiss-Model. 9) Determining putative function of the protein. 10) Submitting to an alert server.

http://www.biocarta.com/

SEQUENCE ANALYSIS:

Step1: Obtain a sequence

To choose a topic of interest

PubMed

 To choose seq of interest you can use the biological databases

www.ncbi.nlm.nih.gov/Entrez/ (Genbank)

http://us.expasy.org/ (Swiss prot)

 Save the seq

Format conversion

http://www.nih.go.jp/~jun/cgi-bin/readseq.pl

Step2:Identify ORF

http://www.softberry.com/berry.phtml(Genefinder)

http://genes.mit.edu/GENSCAN.html  (Genscan)

http://compbio.ornl.gov/Grail-1.3/ (Grail)

Translate in to protein

www.expasy.ch/tools/dna.html

http://www.ebi.ac.uk/emboss/transeq/

 Step3:Find similar seq in databases

www.ncbi.nlm.nih.gov/BLAST/

www.ebi.ac.uk/fasta33

 fasta preferred for nucleotides and blast for proteins.

Also gives local alignment

 Step4:Global alignment

http://www.wadsworth.org/res&res/bioinfo.htm (Bayes block aligner)

http://searchlauncher.bcm.tmc.edu/seq-search/alignment.html (BCM, Pairwise seq alignment)

 Step5:Multiple seq alignment

http://www2.ebi.ac.uk/clustalw/ (Clustal with phylo)

http://blocks.fhcrc.org/blocks/ (Blocks)

http://www.ncbi.nlm.nih.gov/ (Macaw)

 Step6:Presence of specific pattern in protein

Search prosite for profiles using profilescan

http://ulrec3.unil.ch/software/PFSCAN_form.html

http://dna.stanford.edu/emotif/ (motif find)

www.expasy.ch/prosite (PROSITE)

http://www.sanger.ac.uk/Pfam (PFAM)

http://bioweb.pasteur.fr/seqanal/interfaces/hmmbuild.html

 Step7:Find similar seq in other species

http://www.ebi.ac.uk/fasta33 (FASTA)

www.ncbi.nlm.nih.gov/BLAST/ (Spesies specific dbs)

Sstep8:Determine putative structure of protein (protein structure prediction)

www.ncbi.nlm.nih.gov/BLAST (PDB-Blast)

predicting the secondary structure of protein

http://jura.ebi.ac.uk:8888 (Jpred

http://insulin.brunel.ac.uk/threader/threader.html (Threader2)

http://www.bmm.icnet.uk/~3dpssm (3dpssm)

 coil-coil regions using Coils

http://ulrec3.unil.ch/software/Coils_form.html

 Predicting structural features

http://guitar.rockfeller.edu/modeller/modeller.html (MODELLER)

http://www.expasy.ch/swissmod/SWISS-MODEL.html (Swiss-Model)

 Step9:Obtain function of query seq.

http://www.ncbi.nlm.nih.gov/PubMed/

search using the names of proteins revealed by various steps as keyword.

 Step10: If a new seq:

Input in to alert server

http://www.mips.biochem.mpg.de/mips/programs/alret.html