3rd Millennium Services

Please note: This page is not my creation. It was designed by3rd Millenium Services. I placed a copy of it here only to facilitate access to this resource. For full information, please access their website.

If your sequence analysis needs are basic, you are invited to use The Gene Discovery Page for your Bioinformatics solutions. We are pleased to provide you with exclusive access to this award-winning resource that has been in operation since 1996 and has been visited by more that 4 million corporate and academic users. The Gene Discovery Page organizes select web-accessible bioinformatics tools in a coherent fashion. As a company, 3rd Millennium is dedicated to serving your more complex bioinformatics needs through the use of state-of-the art, customized database-driven tools and informatics infrastructure solutions. You are invited to explore our array of available tools that can be tailored to your specifications and to read the success stories of their implementation in diverse settings.

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 SRS server at EMBL (Germany) at WEHI (Australia) at U Indiana (US).
Search a variety of sequence and structure databases using the DBGET server at Kyoto (Japan)

Step 2. Identify ORFs and translate into protein

Genefinder at the Sanger Center (UK).
GENSCAN at MIT (US).
GRAIL at ORNL (US).
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).
AAT at Michigan Tech University (US).

Step 3. Find similar sequences in the databases

Nucleotide sequence: Search the database of your choice using Blast at NCBI (US). Use the blastx option and input the nucleotide sequence 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 aa 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 (eg. "gain" or "loss" of functional domains vis-a-vis a reference sequence.

Pairwise sequence Alignment query at EERIE, France.
Pairwise 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).
Multiple sequence Alignment with phylogenetic tree capabilities using CLUSTAL at EBI (UK).

Step 6. Look for the presence of specific patterns in your protein

Extract a consensus matrix using the concensus server at UniversitÈ Libre de Bruxelles (Belgium).
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).
Generate a consensus from your alignment usingDisplay.

Step 7. Find similar sequences in other species

Search several proteomes using the FASTA search interface at the University of Virginia (US).
Search the SGD (S. cerevisiae) Database using the Blast search feature of SGD at Stanford (US).
Search the AtDB (A. thaliana) Database using the Blast search feature of AtDB at Stanford (US).
Search the Drosophila Genome project sequences using the Blast search feature at EBI (UK).
Search several species-specific databases with Blast at NCBI (US). Use the pull-down menu to select species-specific database

Step 8. Determine the putative structure of your protein

Predict the secondary structure of your protein using the SIMPA server at the NIH.
Predict the secondary structure of your protein using the GOR Secondary Structure Prediction server at the NIH.
Predict the secondary structure of your protein using the Quadratic Logistic Secondary Structure Prediction server at the NIH.
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 9. 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 10. 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).