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Genomic start of the feature, with a 1-base offset. This is in contrast with other 0-offset half-open sequence formats, like BED. 5 end Genomic end of the feature, with a 1-base offset. This is the same end coordinate as it is in 0-offset half-open sequence formats, like BED. [citation needed] 6 score
[2] [3] BAM is the compressed binary representation of SAM (Sequence Alignment Map), a compact and index-able representation of nucleotide sequence alignments. [4] The goal of indexing is to retrieve alignments that overlap a specific location quickly without having to go through all of them.
Wobble base pairs for inosine and guanine. A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules. [1] The four main wobble base pairs are guanine-uracil (G-U), hypoxanthine-uracil (I-U), hypoxanthine-adenine (I-A), and hypoxanthine-cytosine (I-C).
The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. [1] It is a free and open standard with widespread software support and a community of users and developers.
The NEXUS format also allows the storage of data that can facilitate analyses, such as sets of characters or taxa. Many popular phylogenetic programs, including PAUP*, [2] MrBayes, [3] Mesquite, [4] MacClade, [5] and SplitsTree, [6] use this format. Nexus file names typically have the extension .nxs or .nex.
The Gene transfer format (GTF) is a file format used to hold information about gene structure. It is a tab-delimited text format based on the general feature format (GFF), but contains some additional conventions specific to gene information. A significant feature of the GTF that can be validated: given a sequence and a GTF file, one can check ...
Pileup format is a text-based format for summarizing the base calls of aligned reads to a reference sequence. This format facilitates visual display of SNP /indel calling and alignment. It was first used by Tony Cox and Zemin Ning at the Wellcome Trust Sanger Institute , and became widely known through its implementation within the SAMtools ...
Oryza sativa (Rice) is used as a model for cereal biology. It has one of the smallest genomes of any cereal species, and sequencing of its genome is finished. [16] (Agronomy, Molecular biology) Physcomitrella patens. Populus, genus used as a model in forest genetics and woody plant studies. It has a small genome size, grows very rapidly, and is ...