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Free, GPL 3 ? Cross-platform -Mac OS, Linux, Windows Official website: alv No No No Console-based (no GUI), yet with colors. Coding DNA is coloured by codon. FASTA, PHYLIP, Nexus, Clustal, Stockholm: Free, GPL 3 No Cross-platform Official website, see also alv on GitHub: arb: structure editable, show bond in helix sequence regions, 2D molecule ...
Salmon is a software tool for computing transcript abundance from RNA-seq data using either an alignment-free (based directly on the raw reads) or an alignment-based (based on pre-computed alignments) approach. It uses an online stochastic optimization approach to maximize the likelihood of the transcript abundances under the observed data.
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.
Software suite to search and cluster huge sequence sets. Similar sensitivity to BLAST and PSI-BLAST but orders of magnitude faster: Protein: Steinegger M, Mirdita M, Galiez C, Söding J [10] 2017 USEARCH Ultra-fast sequence analysis tool: Both: Edgar, R. C. (2010). "Search and clustering orders of magnitude faster than BLAST". Bioinformatics.
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]
In silico PCR example result with FastPCR [7] [8] software. The design of appropriate short or long primer pairs is only one goal of PCR product prediction. Other information provided by in silico PCR tools may include determining primer location, orientation, length of each amplicon , simulation of electrophoretic mobility, identification of ...
Software by NIST for compression of structure with mass spectra. The program seeks to find mechanisms and their rates for all fragmentation types (EI, Tandem positive and negative mode) and correlates mass spectral peaks to a probable origin structure. It contains an isotope calculator and other features and on-line help.
Parameters for the selected alignment program can then be specified and a progress bar will appear while the tool is being computer. Aligned sequences will replace unaligned ones in the main section of the Alignment Editor. To perform further analysis in MEGA, it is advisable to save the alignment session in either MEGA or FASTA format. [5]