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RSeQC [14] analyzes diverse aspects of RNA-Seq experiments: sequence quality, sequencing depth, strand specificity, GC bias, read distribution over the genome structure and coverage uniformity. The input can be SAM, BAM, FASTA, BED files or Chromosome size file (two-column, plain text file).
GC content is found to be variable with different organisms, the process of which is envisaged to be contributed to by variation in selection, mutational bias, and biased recombination-associated DNA repair. [19] The average GC-content in human genomes ranges from 35% to 60% across 100-Kb fragments, with a mean of 41%. [20]
OLIGO Primer Analysis Software is a software for DNA primer design. [1] [2] The first paper describing this software was published in 1989. [3] The program is a real time PCR primer and probe search and analysis tool. It additionally performs siRNA and molecular beacon searches, open reading frame analysis, and restriction enzyme analysis.
Free, GPL2 ALLALIGN For DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater, MSA or within a single molecule. Similar alignments are grouped together for analysis. Automatic repetitive sequence filter. Both Local E. Wachtel 2017 Free AMAP: Sequence annealing: Both: Global: A. Schwartz and L. Pachter: 2006: BAli-Phy
For example, an oligonucleotide of six nucleotides (nt) is a hexamer, while one of 25 nt would usually be called a "25-mer". Oligonucleotides readily bind, in a sequence-specific manner, to their respective complementary oligonucleotides, DNA, or RNA to form duplexes or, less often, hybrids of a higher order.
Dicey [15] is free software that outputs in-silico PCR products from primer sets provided in a FASTA file. It is fast (through use of a genome's FM-index ) and can account for primer melting temperature and tolerated edit distances between primers and hit locations on the genome.
Bio-Synthesis, Inc. (BSI) is a biotechnology company headquartered in Lewisville, Texas.It is a provider of custom and catalog peptides, custom oligos, antibodies, organic synthesis, and analytical services.
FASTA, Clustal: Free, GPL 3 No Linux Terminal Official website: Ale (emacs plugin) No Yes No No GenBank, EMBL, FASTA, PHYLIP: Free, GPL: No GNU Emacs Official website: AliView 2021 No MUSCLE integrated; other programs such as MAFFT can be defined External programs such as FastTree can be called from within