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IMac – Desktop Mac OS X 10.6.2 2 × 2.Sequence Alignment Software Editor's PicksīioEdit - a free and very popular free sequence alignment editor for Windows. IMac – Desktop Mac OS X 10.6.2 2 × 2.0 Ghz Dualcore Intel Xeon 4 Gb 1 TB DB Administration #Codoncode aligner ver. 2 pro#Mac Pro – Desktop Mac OS X 10.6.2 2 × 2.6 Ghz Quadcore Intel Xeon 10 Gb 1 TB Sequences Analysis. #Codoncode aligner ver. 2 code#Power Mac G5 Mac OS X 10.4.11 Dual 2.7 Ghz Power Mac G5 2.5 Gb 500 GB InterProScan, Blast, Codon Code Aligner IBM Xseries 345 Suse Enterprice Server 10 SP1 2 × 3.06 Ghz Intel Xeon 4 Gb 280 GB Public web server IBM e325 Ubuntu Desktop 9.10 32 b 2 × 2.4 Ghz AMD Opteron 5 Gb 65 GB Mira IBM e325 Ubuntu Server 2 × 2.4 Ghz AMD Opteron 5 Gb 65 GB Test server ![]() IBM e325 Ubuntu Server 2 × 2.4 Ghz AMD Opteron 5 Gb 65 GB 454 Server IBM e325 Ubuntu 8.10 2 × 2.4 Ghz AMD Opteron 5 Gb 65 GB Mapping Server, FPC Sunfire-V240 Solaris 5.1 2 × 1.0 Ghz 4 Gb 140 GB Assembly IBM Xseries 346 Linux Suse 10 SP1 4 × 3.6 Ghz Intel Xeon 5 Gb 1.1 TB Web Server, DB Server, GBrowse, Blast, tgicl, Emboss, Bioperl Type Operative System Processor RAM Hard Disc Functionality – ApplicationĪpple XServe Mac OS XServer 10.5.8 2 × 3.0 Ghz Quadcore Intel Xeon 4 Gb 1.78 TB InterProScan, Blast, SGE, orthomclĪpple XServe Mac OS XServer 10.5.8 2 × 2.0 Ghz Dualcore Intel Xeon 4 Gb 1.78 TB InterProScan, Blast, SGE, orthomcl Ideally, these approaches co-exist and complement each other in the same annotation pipeline.įor data analysis and processing at Cenicafé we use the following machines: curation) which involves human expertise. #Codoncode aligner ver. 2 manual#Identifying elements on the genome, a process called gene prediction, and attaching biological information to these elements.Īutomatic annotation tools try to perform all this by computer analysis, as opposed to manual annotation (a.k.a. Genome annotation is the process of attaching biological information to sequences. These overlapping reads can be merged together, and the process continues. (The four bases are adenine, guanine, cytosine, and thymine, represented as AGCT.) A genome assembly algorithm works by taking all the pieces and aligning them to one another, and detecting all places where two of the short sequences, or reads, overlap. These pieces are then “read” by automated sequencing machines, which can read up to 900 nucleotides or bases at a time. In a shotgun sequencing project, all the DNA from a source (usually a single organism, anything from a bacterium to a mammal) is first fractured into millions of small pieces. Genome assembly refers to the process of taking a large number of short DNA sequences, all of which were generated by a shotgun sequencing project, and putting them back together to create a representation of the original chromosomes from which the DNA originated. ![]() Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning different DNA and protein sequences to compare them and creating and viewing 3-D models of protein structures. It is the name given to these mathematical and computing approaches used to glean understanding of biological processes. Over the past few decades rapid developments in genomic and other molecular research technologies and developments in information technologies have combined to produce a tremendous amount of information related to molecular biology. Bioinformatics now entails the creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data. Its primary use since at least the late 1980s has been in genomics and genetics, particularly in those areas of genomics involving large-scale DNA sequencing. The term bioinformatics was coined by Paulien Hogeweg in 1979 for the study of informatic processes in biotic systems. Bioinformatics is the application of computer science to the field of molecular biology. ![]()
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