FASTA sequence file

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). 

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. 

Fasta is a popular file format for DNA sequences. A Fasta format file may contain one or more sequences. Each sequence has a header line that begins with the character > followed (without spaces) by an identifier (e.g., name) for that sequence, and other descriptive text (if any) following the identifier. Following each header line are one or more lines of DNA sequence. See the file ROOT/data/cer.fna for an example. 

The two sequence files are required to be in Fasta format and should contain exactly the same number of sequences, in the exact same order (i.e., ordered by orthologous pairs). However, orthologous upstream regions need not have the same name. 

Connect notation (ct) it provides a textual description of the basepairings. The syntax is as follows columns 1, 3, 4, and 6 redundantly give sequence indices, column 2 gives the sequences and column 4 gives j in position i if (i,j) is a basepair, otherwise this is zero. The heading of the file contains the size of the sequence and its name (found in the FASTA sequence). 

The impredict algorithm uses a two-layer, feed-forward neural network to assign the predicted type for each residue (Kneller et al., 1990). In making the predictions, the server uses a FASTA format file with the sequence in either one-letter or three-letter code, as well as the folding class of the protein (a, j8, or a//8). Residues are classified... 

The result of a query will be a table of summarized results, including name, cytological location, accession number, or Bloomington stock number each name hyperlinks to a full report (described below for each data type under Scope of FlyBase Data Types). The results can be saved as a text file for import into any common spreadsheet software that can interpret tab-delimited files (such as Excel or Filemaker), or as a FASTA formatted file of the sequences for sequence analysis. 

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. 

Study the nucleotide sequence for the gene coding for human a-lactalbumin. Hint Begin at the NCBI home page and enter Entrez. Click on Nucleotides and do a search on human a-lactalbumin. Review the GenBank report for the position of introns and exons. Obtain a FASTA report, transfer (download) the files, and complete a BLAST search for related sequences. 

The most frequent problems are related to input file formats. The sequence format used by the Vienna RNA package is very similar to FASTA, except that no line breaks or whitespace are allowed in the sequence. Line breaks will cause each... 

NGS machines usually produce raw data files in FASTA or FASTQ format, which contain millions of short-sequence reads. A significant level of computational expertise is thus required for the analysis of NGS small RNA-seq datasets, with many command line and web-based analysis platforms available (Table 2). Following sequencing, quality is assessed in order to determine whether the sequencing run was successful. Resources for... 

Retrieve nucleotide sequences (fasta files) of yeast cytosolic and mitochondrial Gly-tRNA and submit them to RNA folding to obtain their secondary (cloverleal) structures and thermochemical data of foldings. 

Retrieve nucleotide sequence (fasta file) and atomic coordinates (pdb file) of yeast Asp-tRNA. Perform folding analysis/molecular modeling to display graphics of the following ... 

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. 

Fig. 2. Each sequence can be pasted in, in FASTA format, uploaded as a FASTA file, or entered as an accession number along with the available annotation (A). Alternatively, sequences can be fetched from the UCSC Genome Browser individually using the Upload function (A), or in groups (Batch Upload System) Browser (B). Once sequences have been uploaded, the program acknowledges the receipt (C).

---