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C++ based molecule editor and visualizer for in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. Linux, macOS, Unix, Windows: 3-Clause BSD License: Open Chemistry Project: BEDtools "Genome arithmetic"—manipulation of coordinate sets and the extraction of sequences from a BED file. Linux: MIT
RNA-Seq [1] [2] [3] is a technique [4] that allows transcriptome studies (see also Transcriptomics technologies) based on next-generation sequencing technologies. This technique is largely dependent on bioinformatics tools developed to support the different steps of the process.
The term transcriptome is a portmanteau of the words transcript and genome; it is associated with the process of transcript production during the biological process of transcription. The early stages of transcriptome annotations began with cDNA libraries published in the 1980s. Subsequently, the advent of high-throughput technology led to ...
It is optimized for short reads such as that generated by Illumina and is capable of assembling large genomes such as the human genome. [2] SOAPdenovo was used to assemble the genome of the giant panda. [3] This was upgraded to SOAPdenovo2, which was optimized for large genomes and included the widely used GapCloser module. [4]
It computes whole genome predictions by mix of distinct whole genome IntaRNA predictions. Yes: Yes: sourcecode webserver [110] [106] MINT Automatic tool to analyze three-dimensional structures of RNA and DNA molecules, their full-atom molecular dynamics trajectories or other conformation sets (e.g. X-ray or NMR-derived structures).
Genome-guided assembly (sometimes mapping or reference-guided assembly) - is capable of using a pre-existing reference to guide the assembly of transcripts Both methods attempt to generate biologically representative isoform-level constructs from RNA-seq data and generally attempt to associate isoforms with a gene-level construct.
Fast detection of coding regions in short genome sequences: Dragon Promoter Finder Program to recognize vertebrate RNA polymerase II promoters: Vertebrates [7] EasyGene: The gene finder is based on a hidden Markov model (HMM) that is automatically estimated for a new genome. Prokaryotes [8] [9] EuGene: Integrative gene finding: Prokaryotes ...
A transcriptome captures a snapshot in time of the total transcripts present in a cell. Transcriptomics technologies provide a broad account of which cellular processes are active and which are dormant. A major challenge in molecular biology is to understand how a single genome gives rise to a variety of cells.