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BLASTN BLAST's nucleotide alignment program, slow and not accurate for short reads, and uses a sequence database (EST, Sanger sequence) rather than a reference genome. BLAT: Made by Jim Kent. Can handle one mismatch in initial alignment step. Yes, client-server Proprietary, freeware for academic and noncommercial use [36] 2002 Bowtie
Command-line utility for predicting alternative (secondary) configurations of riboswitches. It is based on the prediction of the so-called switching sequence, to subsequently constrain the folding of the two functional structures. No: sourcecode [36] UFold: UFold: fast and accurate RNA secondary structure prediction with deep learning: Yes
The Smith-Waterman option provides better accuracy, in that it finds matches that BLAST cannot, because it does not exclude any information. Therefore, it is necessary for remote homology. However, when compared to BLAST, it is more time consuming and requires large amounts of computing power and memory.
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. [1]
In computer programming, a usage message or help message is a brief message displayed by a program that utilizes a command-line interface for execution. This message usually consists of the correct command line usage for the program and includes a list of the correct command-line arguments or options acceptable to said program.
A command prompt (or just prompt) is a sequence of (one or more) characters used in a command-line interface to indicate readiness to accept commands. It literally prompts the user to take action. A prompt usually ends with one of the characters $ , % , # , [ 15 ] [ 16 ] : , > or - [ 17 ] and often includes other information, such as the path ...
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.
MEGA is in two version. A graphical user interface is available as a native Microsoft Windows program. A command line version, MEGA-Computing Core (MEGA-CC), is available for native cross-platform operation. The method is widely used and cited. With millions of downloads across the releases, MEGA is cited in more than 85,000 papers.