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advanced publication date as opposed to the date of publication) The current FASTA package contains programs for protein:protein, DNA: DNA, protein:translated DNA (with frameshifts), and ordered or unordered peptide searches.
Recent versions of the FASTA package include special translated search algorithms that correctly handle frameshift errors (which six-frame-translated searches do not handle very well) when comparing nucleotide to protein sequence data.
Grey dotted lines connect related mappers (extensions or new versions).
The timeline only includes mappers with peer-reviewed publications, and the date corresponds to the earliest date of publication (e.g.
Total RNA was prepared using TRIzol reagent (Invitrogen) and TURBO DNase (Ambion).
Total RNA was used to synthesize c DNA with random primers.
The cluster is managed by the UVa Advanced Research Computing Services (ARCS) group.
Usage of rivanna is metered in terms of "service units" (currently equal to the number of hours used), with each research group being allocated some number of service units.
This series contains CAGE peaks only for the HBV genome.About the Rivanna Cluster: In 2014, the College of Arts and Sciences, the Engineering School, the UVa Library and the Data Science Institute purchased a powerful new computing cluster called "rivanna".If you do computationally intensive work, you might benefit from using it.The size taken for a word, given by the parameter kmer, controls the sensitivity and speed of the program.
Increasing the kmer value decreases number of background hits that are found.There are some differences between fastn and fastp relating to the type of sequences used but both use four steps and calculate three scores to describe and format the sequence similarity results.