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Although the FASTA format is most often used as input to formatdb, the use of ASN.1 is advantageous for those who are using ASN.1 as the common source for other formats such as the GenBank report. The opposite of operation of formatdb, extracting sequences from a blast formatted database, can be achieved by using the fastacmd program, which ...
The original FASTA/Pearson format is described in the documentation for the FASTA suite of programs. It can be downloaded with any free distribution of FASTA (see fasta20.doc, fastaVN.doc, or fastaVN.me—where VN is the Version Number).
The input can be SAM, BAM, FASTA, BED files or Chromosome size file (two-column, plain text file). Visualization can be performed by genome browsers like UCSC, IGB and IGV. However, R scripts can also be used for visualization. SAMStat [15] identifies problems and reports several statistics at different phases of the process. This tool ...
Gary Kessler's list of file signatures; Online File Signature Database for Forensic Practitioners, a private compilation free to Law Enforcement; Man page for compress, uncompress, and zcat on SCO Open Server; Public Database of File Signatures; Complete list of magic numbers with sample files
A FASTQ file has four line-separated fields per sequence: Field 1 begins with a '@' character and is followed by a sequence identifier and an optional description (like a FASTA title line). Field 2 is the raw sequence letters. Field 3 begins with a '+' character and is optionally followed by the same sequence identifier (and any description) again.
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. [1] Its legacy is the FASTA format which is now ubiquitous in bioinformatics .
MATLAB (an abbreviation of "MATrix LABoratory" [18]) is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks.MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages.
As sorting is memory intensive and BAM files can be large, this command supports a sectioning mode (with the -m options) to use at most a given amount of memory and generate multiple output file. These files can then be merged to produce a complete sorted BAM file [TODO - investigate the details of this more carefully].