Free Services: Selection of Antigenic Peptides, BLAST searches (PSSA)

ADI is a global company providing custom peptide and antibody services throughout the US and many international institutions. ADI's services have been referenced in most top-ranked scientific journals.

Free Services: Selection of Antigenic Peptides, BLAST searches, Identification of Signal peptide, Transmembrane domains, Sequence Alignment, and other common structural motifs.

ADI Inc. has been providing FREE and no-obligatory consultation service to Scientists around the globe to find specific antigenic peptides from long protein sequences. We realize that many researchers either do not have necessary tools, computers programs, and expertise or simply do not wish to invest time in analyzing protein sequences. We now offer the following services.

1. Identification of specific antigenic peptides. Analyses of complete or partial protein sequences to find antigenic peptides. Our recommendations are based upon the analyses of antigenicity, hydrophilicity, and accessibility parameters. We try to find peptide regions (10-25 aa) that are antigenic, hydrophilic, and accessible. This information is sent in an easy to understand graphical format by email or fax. The regions will be identified by upward peaks on various graphs. This increases the likelihood of generating an antibody that recognizes the full length protein. Click here for examples of a typical antigenicity, hydrophilicity, and accessibility plots.

2. BLAST searches. All recommended antigenic peptides are then subjected to BLAST to confirm specificity of peptides. This is extremely important since short peptides may show higher degree of amino acid homology with either related members or unrelated proteins creating unwanted antibody crossreactivity. Although, ADI has rather broad knowledge about many disciplines, investigators must decide if homology to a given protein as shown in BLAST is problematic or not. This info is typically sent by email. We recommend that each peptide sequence intended for antibody production MUST be subjected to BLAST. This identifies proteins to which antibody may crossreact. It is very important to carefully review this information. Since we may not complete knowledge of a given protein and related members, researchers must decided if peptide homology to a given protein is problematic or not. (Click here for an example of BLAST)

3. ADI may also analyze the protein secondary structure (see section 4). Based upon the available information, we typically suggest 1-4 peptides (10-25 AA) that are suitable for antibody production.

4. Proteins Secondary Structure Analyses (PSSA). A given protein contains one or more of the following.

• Signal peptide (GvH: von Heijne's method for signal seq. Recognition)
• Transmembrane domains (ALOM: Klein et al's method for TM region allocation)
• Mitochondrial targeting seq. (MITDISC)
• Nuclear localization signals (NUDISC)
• ER retention motif (KDEL)
• Peroxisomal targeting signal in the C-terminus (SKL/SKL2)
• Vacuolar targeting motif (VAC)
• Actinin-type actin-binding motif
• N-myristoylation pattern (NMYR)
• Prenylation motif
• Transport motif from cell surface to Golgi (memYORL)
• Tyrosines in the tail and Dileucine motif
• PROSITE DNA binding motifs Leucine zipper pattern
• PROSITE ribosomal protein motifs
• Reinhardt's method for Cytplasmic/Nuclear discrimination
• Lupas's algorithm to detect coiled-coil region

We will analyze the sequence using appropriate computer programs to predict/identify the presence of common structural protein motifs. This information is very important in identifying the antigenic peptide and targeting antibodies to a desired domain. This info also helps in identifying the possible functions of proteins. We will send our analyses by email or fax. (Click here for an example of Protein Secondary Structure Analyses (PSSA).

5. Multiple Sequence alignment using ClustalW . It is sometime necessary to produce multiple sequence alignments for 2 or more related proteins. It helps in identifying specific antigenic peptides and avoiding potential antibody crossreactivity. It is also useful in determining overall amino acid homology and identifying conserved regions. A multicolored sequence alignment is sent that shows conserved amino acid and % identity among the proteins. (Click here for an example of multiple sequence alignment using ClustalW).

How to submit sequence to us for analyses (On-line PSSA form ).

Please send your name, complete address, phone, fax, email addresses preferably by email or fax. We will send our analyses by email or fax within 1-3 days. All information provided to us remain confidential. If you wish to submit a sequence for the identification of antigenic peptides for making antibodies, please provide the following information by email. Please do not forget to include your phone and fax #.

1. Name (S) of the protein, gene accession # (if available), and amino acid sequence (single letter code) by email.

2. Sequence alignment of all related proteins, if available, by fax. This will help us in avoiding regions that are conserved.

3. Any preference for targeting peptides (amino terminal, c-terminal). You can also specify regions to avoid.

4. You can mention any peptide(s) that you have already selected.

For secondary protein structure analyses. Please send the name, gene accession number, species (bacterial, plant, yeast, animals) and actual amino acid sequence (single letter code) of sequence by email.

For Multiple sequence alignment. Please send the name, gene accession number, and actual amino acid sequence (single letter code) of ALL proteins.

For BLAST searches. Please send the peptide sequence by email along with the name of the gene, gene accession number, if any. We typically search using the "nr" databases.

ADI is glad to be of service to our fellow Scientists. There is no-obligation to buy anything from us. But if you do need peptides or antibodies, please take a look at our services. We believe that you will not find more reliable or economical source.

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