Step 1: obtaining a sequence of interest
If you have a sequence of interest proceed to step 2.
Once you obtained your sequence of interest (YSI) save it in a file using the "Save As" command of your browser.
- Search PubMed, a public version of full Medline for topics of interest (US).
- Search Genbank for sequences of interest (US).
- Search protein and nucleic acid databases using Atlas at MIPS (Germany).
- Search a variety of sequence and structure databases using the SRSWWW server at EMBL (Germany).
Step 2. Identify ORFs and translate into protein
- DNA sequence translation page at the University of Minnesota (US).
- Gene feature searches at Baylor College of Medicine (US).
- GenLang searches at University of Pennsylvania (US).
- DNA sequence translation into protein
tool at ExPaSy (Switzerland).
Step 3. Find similar sequences in the databases
- Nucleotide sequence: Search the database of your choice
Blast at NCBI (US).
Use the blastx option and input the nucleotide sequece of your ORFs.
- Protein sequence: Search the database of your choice using
Blastp + Beauty at Baylor College of Medicine (US). Input the translated aa sequence of your ORFs.
- Protein sequence: Search the database of your choice using The BIOCCELERATOR at the Weizmann Institute (Israel). Input the translated amino acid sequence of your ORFs.
Step 4. Do a global alignment of your sequence vs similar sequences
Even though, the previous Blast search engines provide local alignments (alignments of the similar regions), a global alignment (alignment of all regions) may help getting a better insight about your target sequence. For example, "gain" or "loss" of functional domains (ivis-a-vis) a reference sequence.
- Pairwise sequence Alignment query at EERIE, France.
- Paiwise sequence Alignment query at Baylor College of Medicine (US).
Step 5. Look for gene families
- Multiple sequence Alignment query at Baylor College of Medicine (US).
- Analyze multiple sequence alignments at the AMAS server at Oxford University (UK).
- Get visual information about the aligned regions at the BOXSHADE server at ISREC (Switzerland).
Step 6. Look for the presence of specific patterns in your protein
- Search the Procite library for profiles using the ProfileScan server at ISREC (Switzerland).
- Search the Blocks database at Fred Hutchinson Cancer Research Center (US).
- Search databases using Motif at GenomeNet (Japan).
- Look for a pattern you define using PatScan at Argonne National Laboratories (US).
- Predict protein sorting signals using the Psort server at the Institute for Molecular and Cellular Biology, Osaka University (Japan).
- Do a statistical analysis of your protein sequence using the SAPS server at ISREC (Switzerland).
Step 7. Determine the putative structure of your protein
- Predict the secondary structure of your protein using the PredictProtein server at the EMBL (Germany).
- Predict the secondary structure of your protein using NNPREDICT at the University of California in San Francisco (US).
- Predict the secondary structure of your protein using the ppsp server at Baylor College of Medicine (US).
- Look for coil-coil regions using the Coils server at ISREC (Switzerland).
Step 8. Obtain information about function of related proteins
To understand the function of your target protein, it may be useful to gather information about proteins that share similar structural or sequence elements.
Thus, a PubMed search using as keywords the names of the proteins revealed by the various steps of this analysis, may provide you with functional insight about your protein.
Step 9. Input your sequence into an "alert" server
"Alert" servers will send you a message if a sequence similar to yours has been inputed in a database.Choose from the following servers:
- Sequence Alerting server at the EMBL (Germany).
- MIPS alert server at MIPS (Germany).
- Swiss-Shop server at ExPaSy (Switzerland).