Fasta format

To improve this unsatisfying situation, many bioinformatics sites construct nonredundant databases from a number of component databases, or they use external nonredundant databases, e.g., OWL (Bleasby et al., 1994). Both strategies considerably improve the situation for the end user, but they require the time- and resource-consuming maintenance of multiple databases or the acceptance of a certain time lag between creation of an entry and its appearance in the nonredundant database. Furthermore, both strategies lead to a loss of information in the individual entry owing to the diversity of database formats. Whereas OWL preserves most information of an entry and some of its structure, the NRDB program requires a conversion of the component databases to FASTA format, which contains only one description line per entry. 

SPTR is distributed in three files sprot.dat.Z, trembl.dat.Z, and trembl new.dat.Z. These files are, as indicated by their Z extension, Unix compress format files, which, when decompressed, produce ASCII files in SWISS-PROT format. Three others files are also available (sprot.fas.Z, trembl.fas.Z, and trembl new.fas.Z), which are compressed fasta format sequence files that are useful for building the databases used by FASTA, BLAST, and other sequence similarity search programs. These files should not be used for other purposes, because all annotation is lost when using this format. The SPTR files are stored in the directory /pub/databases/sp tr nrdb on the EBI FTP server (ftp.ebi.ac.uk) and in the directory /databases/sp tr nrdb on the ExPASyFTP server (ftp. expasy.ch). 

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 4.4. Fasta format for nucleotide 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. 

Retrieve nucleotide sequences (in fasta format) and restriction maps for one each of bacterial plasmid, cosmid and shuttle vector. 

Retrieve DNA encoding human alcohol dehydrogenase isozymes in fasta format and perform multiple alignment with ClustalW. 

EMBL Nucleotide Sequence Database. SWISS-PROT consists of core sequence data with minimal redundancy, citation and extensive annotations including protein function, post-translational modifications, domain sites, protein structural information, diseases associated with protein deficiencies and variants. SWISS-PROT and TrEMBL are available at EBI site, http //www.ebi.ac.uk/swissprot/, and ExPASy site, http //www.expasy.ch/sprot/. From the SWISS-PROT and TrEMBL page of ExPASy site, click Full text search (under Access to SWISS-PROT and TrEMBL) to open the search page (Figure 11.3). Enter the keyword string (use Boolean expression if required), check SWISS-PROT box, and click the Submit button. Select the desired entry from the returned list to view the annotated sequence data in Swiss-Prot format. An output in the fasta format can be requested. Links to BLAST, feature table, some ExPASy proteomic tools (e.g., Compute pI/Mw, ProtParam, ProfileScan, ProtScale, PeptideMass, ScanProsite), and structure (SWISS-MODEL) are provided on the page. 

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 sequence data, in Phylip format, should be in an input hie called infile within the package. Use ReadSeq at http //dot.imgen.bcm.tmc.edu 9331/seq-util/ Options/readseq.html to convert retrieved sequences in any formats (e.g., fasta format) to Phylip3.2 format. Copy and paste the sequence set, select Phylip3.2 as the output format, and click the Perform conversion button. From the output, copy only the identiher (number of species and number of characters), species name, and characters (sequences) into the inhle (Figure 13.2). 

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. 

Download the trial sequence in fasta format (start with >) and save it as trialseq.txt. 

If it is necessary to upload sequence files, these can be compressed using either WinZip, or the UNIX gzip utility, which will significantly reduce the time taken to upload the data. Submitted files should each contain a single sequence in EMBL or FASTA format. It is preferable to use EMBL/Genbank format for uploaded sequences, because any genes annotated in the feature table will then be displayed by ACT. Should multiple sequences be present in an uploaded file, only the first will be used. 

Prepare unannotated target genome sequence in FASTA format. 

To obtain the query and target sequences in FASTA format, click the Show button. The sequences can then be copied and pasted into a word processor or text editor as desired. 

For efficiency purposes, we need to put our FASTA-formatted sequences into another format. The author has developed a file format, the Sequence Database format (SDB), that allows for fast random access to multiple sequences stored in a single file. See Note 2b for descriptions of the command-line utilities available (as part of the Mercator distribution) for creating and accessing SDB files. We will use the fa2sdb utility to put our softmasked genomes into SDB format. 

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