Amino acid sequences retrieving

The amino acid sequences of proteins and nucleotide sequences of DNA can be retrieved from the integrated database retrieval systems Entrez (http //... 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

Figure 11.6. Amino acid sequence alignment at EBI. Amino acid sequences of type C lysozyme are submitted to ClustalW tool of EBI, and the alignment is retrieved from the notified URL...

Retrieve amino acid sequences (in fasta format) of human alcohol dehydrogenase isozymes and perform multiple alignment with ClustalW to evaluate their homology. Identify the amino acid substitutions among the seven isozymes. 

Retrieve the amino acid sequences of liver alcohol dehydrogenase from six organisms to perform phylogenetic analysis. Compare phylogenetic results from Fitch-Margoliash methods without (Fitch) versus with (Kisch) molecular clock using the Dayhoff PAM 001 matrix. 

Retrieve the amino acid sequences of type C lysozymes from twelve biological sources. Perform ClustalW multiple sequence alignment and WebPhylip parsimony analysis to draw a cladogram of the consensus tree. 

Retrieve pdb file of ribonuclease A and use it as the reference coordinates to perform homology modeling of sheep ribonuclease A with the following amino acid sequence ... 

Go to the SWISS-MODEL Web site (http //www.swissmodel. expasy.org), select Automated Mode, input the e-mail address and the amino acid sequence of the protein retrieved from the Protein Information table, and click Submit Modeling Request to build target protein structure. (See the crystal structure of SpoVT AbrB (pdb code 2W1T) for Bacillus subtilis in Fig. 1.)... 

A mixture as claimed in claim 1, wherein the mixture contains 160000 or more different peptides of distinct, unique and different amino acid sequences, each in retrievable andanalyzable amounts. 

A mixture of 8000 or more peptides with distinct, unique and different amino acid sequences, which mixture contains each of the 8000 or more peptides in retrievable and analyzable amounts, the mixture being produced by a process, comprising ... 

For the synthetic library method that uses the affinity chromatography selection approach, the bound peptides can be eluted and microsequenced by Edman degradation. Concurrent microsequencing of the retrieved peptide mixture can be performed rather than sequencing individual peptides. Sequeuce motifs then can be defined in a fast and efficient way. However, the amino acid sequence obtained wiU be the result of the summation of the peptide mixture. Uuless a predomiuaut, distinct motif and an alignment of one or more of the critical residues exists within the peptide sequence of the library (e.g., with a fixed residue at a specific position), the result could be very difficult if not impossible to interpret. 

How to Retrieve the Amino Acid Sequence from a Mass Spectrum 475... 

The task of retrieving the amino acid sequence from a mass spectrum involves arranging certain ions into a sequence-specific series, for example, either into the j-ion series or b-ion series. The following steps are helpful in this exercise ... 

GeneSeq . Thomson Derwent s biosequence database, provides information on nucleic and amino acid sequences found in the patent literature. It has biosequence indexing for the patents included in the DWPI database beginning with the very first patents to carry protein and nucleotide sequence descriptions. GeneSeq structure searches retrieve records with the sequence, a short abstract directed to that sequence. 

Protein Identification Resource National Biomedical Research Foundation Georgetown University Medical Center 3900 Reservoir Road, N.W., Washington, DC 20007 Contains nucleotide and amino acid sequences not as extensive in nucleotide sequences as EMBL-GenBank good program environment for quick and easy data retrieval... 

Besides such textual databases that provide bibhographic information, sequence databases have attained an even more important role in biochemistry. Sequence databases are composed of amino add sequences of peptides or proteins as well as nudeotide sequences of nudeic acids. The 20 amino adds are mostly represented by a three-letter code or by one letter according to the biochemical conventions) the four nudeic adds are defined by a one-letter code. Thus the composition of a biochemical compound is searchable by text retrieval methods. 

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