FASTA file format

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... 

Pathway Tools can export PGDBs into several different file formats that are described at http //bioinformatics.ai.sri.com/ ptools/flatfile-format.html. These formats include column-delimited tables, SBML (see http //sbml.org/), BioPAX (see http //biopax.org/), Genbank, FASTA, and attribute-value. 

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).

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. 

In most cases, data presented by this software is calculated based on the ORF or ORF set selected in the left panel of the main window. If a special set of ORFs is to be analyzed it must be formatted as a FASTA file containing the chosen ORFs and then be opened by ANACONDA at later stage. 

The following example shows how BioPerl can be used to read protein sequences from a FASTA file and find signal peptide cleavage sites. The file format is inferred from the file extension. fa. 

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. 

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... 

Like FASTA, BLAST has also been adapted to connect good diagonals and report local alignments with gaps. BLAST converts the database file into its own format to allow for faster reading. This makes it somewhat unwieldy to use in a local installation unless someone takes care of the installation. FASTA, on the other hand, is slower but easier to use. There exist excellent web servers that offer these programs, in particular at the National Center for Biotechnology Information (NCBI [59]) and at the European Bioinformatics Institute (EBI [60]) where BLAST or FASTA can be used on up-to-date DNA and protein databases. 

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. 

In the Files box there are options to see and download the DIALIGN aligned sequences either in multiple fasta or dialign format. 

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. 

Gibbs accepts sequence data in FASTA format. The Gibbs distribution contains a sample data file, crp.dat. This file, along with all data files used in this article, is available for download at http //bayesweb.wadsworth.org/ gibbs/module. 

If sequences were prepared outside the CONREAL framework (see Note 1), paste them in FASTA format in the text window (Fig. 1A) or provide a name of the file with the sequences (plain text file containing two sequences in FASTA format) (Fig. IB). Proceed to Subheading 3.2. 

Fig. 1. CONREAL sequence input form. (A) Two sequences in Fasta format can be pasted into the text field or (B) provided in a plain text file or (C) sequences can be automatically retrieved from the Ensembl database using a gene name or keyword and a species name.

Data the genomes files processed by the ANACONDA must be in FASTA format. 

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