Amino acids FASTA

How does one go about finding all of the relevant proteins in a database once it has been decided to carry out an analysis of an entire protein family The simplest approach is to use similarity search software such as SSEARCH or FASTA (Smith and Waterman, 1981 Pearson and Lipman, 1988) or BLAST (Altschul et al, 1997) with the amino acid sequences of one or two well-known members of the family as queries. The problem is initially the same as that of identifying all proteins that are homologous to a family of proteins, although with some important practical differ-... 

Another useful structure tool is RasMol (or RasMac). This will allow you to view the detailed structure of a protein and rotate it on coordinates so you can see it from all perspectives. A hyperlink to RasMol is present under the View Structure function just above Chime. You may need to study RasMol instructions provided under Help, or you may use a Ra.s Mol tutorial listed in Table El.2. Another useful protein viewer is tin-Swiss-Protein Pdv Viewer (Table El.2). BLAST is an advanced sequence similarity tool available at NCBI. To access this, go to the NCBI home page (www.ncbi.nlm.nih.gov) and click on BLAST. Then click on Basic BLAST search to obtain a dialogue box into which you may type the amino acid sequence of human a-lactalbumin. This process may be stream lined by downloading the amino acid sequence in FASTA format into a file and transferring the fde into the BLAST dialogue box. BLAST will provide a list of proteins with sequences similar to the one entered. 

Figure 4.8. Fasta format for amino acid sequence of chicken egg-white lysozyme.

The ID nucleotide/amino acid sequences in character format (without index, e.g., fasta format) can be converted into the 2D chemical structures with ISIS Draw, which can be downloaded from MDL Information System at http //www.mdli.com/ download/isisdraw.html for academic use. Install the package by issuing Run command, C Isis Draw23.exe. Launch IsisDraw to open the Draw window. 

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. 

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. 

The 3D-ID compatibility algorithm (Ito et ah, 1997) is applied to predict the secondary structures by threading at SSThread of DDBJ (http //www.ddbj.nig.ac.jp/ E-mail/ssthread/www service.html). Paste the query sequence (fasta format) into the sequence box, enter your e-mail address, and click the Send button. The e-mail returns the threading result reporting the amino acid sequence with the predicted secondary structures (H for a. helix, E for / strand, and C for coil or other). 

The biopolymer modeling of HyperChem includes Building polynucleotides, polypeptides and polysaccharides, Amino acid sequence (fasta format) editing, Mutations, Overlapping by RMS fit, and Merging structures. To facilitate manipulation of protein structures, there is often a need to display the protein backbone only as follows. 

Fig. 2. Edited portion of the FASTA search of the NBRF database (release date September 1990) using the amino acid translation of the large open reading frame of the Uhu element from D. heteroneura. This shows that the first two matches are nearly identical and that they are dearly superior to any other matches found. The alignment to the Tel dement transposase is shown.

Ladies GS, Bannon GA, Silvanovich A, Cressman RF. Comparison of conventional FASTA identity searches with the 80 amino acid sliding window FASTA search for the elucidation of potential identities to known allergens. Mol Nutr Food Res. 2007 51(8) 985-998. 

It should be noted that, for both global and local alignment, the time complexity is 0(nm), highly computationally expensive, in particular for clustering problems (Xu and Wuncsh, 2005) or when processing a large volume of nucleic acids and amino acid sequences in a database. Alternatively, sequence comparison could be achieved via heuristic approaches, such as FASTA, BLAST, and their variants (Altschul et al., 1990, 1997 Lipman and Pearson, 1985 Pearson and Lipman, 1988). To achieve low... 

Furthermore, two files were generated containing the amino acid sequences of 684 fly and 405 worm translation products in FASTA format identified in the above screen. Batch BLASTp analysis of the fly protein set versus the worm protein set and vice versa was performed using locally installed stand-alone BLAST program (59). Genes represented in both data sets, termed HRE relatives, are listed in Table 2 ( Both table). Selected results for the individual fly and worm data sets can be found in Table 3 ( Fly table ) and Table 4 ( Worm table ). The entire fly and worm data sets are available as supplementary information at http //bium.bwh.harvard.edu/ with entries categorized by function. 

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