Download Bioinformatics: Methods and Protocols by Stephen Misener, Stephen A. Krawetz PDF

By Stephen Misener, Stephen A. Krawetz

Hands-on clients and specialists survey the most important organic software program applications, delivering valuable advice and an outline of present advancements. one of the series research platforms reviewed are GCG, Omiga, MacVector, DNASTAR, PepTool™, GeneTool™, and the Staden package deal. Molecular biology software program contains Genotator and sequence-similarity looking utilizing FASTA, CLUSTAL a number of series alignment, and phylogenetic research. Web-based assets are tested for basic series databases, basic series research tools, and medical databases priceless in molecular medication. quite a few illustrative examples to coach the reader easy methods to clear up difficulties are incorporated. Bioinformatics: tools and Protocols constitutes a gold-standard reference for contemporary scientists who desire to strengthen and hone their bioinformatics abilities in the direction of the invention of recent organic relationships.

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1. Projects Omiga uses a project concept to organize sequences, their individual notations, and any additional results and information generated for those sequences by the program. A project represents a simple way to organize an individual investigator’s data. Different projects can be localized onto different sectors of the hard drive, or even on a remote storage device such as a Zip drive. Multiple users can also use several separate projects to organize unrelated sequences, and sequence from unrelated lab projects to reduce the amount of superfluous data in each individual interface.

Omiga 1 comes with an internal copy of the GENMOTIFS database. In addition, sequences characteristic of genes (gene-associated motifs) can be added by the user. For example, it has been suggested that uneven positional base preference can be used as an accurate indicator of expressed segments within large genomic sequences (3). Whereas this may be difficult to fashion into a gene-associated motif, it is conceivable that other motifs may be identified that are characteristic of coding regions. It appears that the search for coding regions in Omiga represents a more complex version of this search protocol, utilizing a search for multiple weighted motifs.

By double clicking on an individual sequence within the tree panel of the project view, a sequence view is opened for the selected sequence. The sequence view can be used to edit a sequence by hand. This feature can be used to reflect site-specific mutations introduced into the sequence in the laboratory as well as sequence polymorphisms. The edited sequence can then be used to identify new restriction sites generated by the specific alterations. Editing can also be used to add a large piece of one sequence to another sequence to reflect cloning experiments in the laboratory.

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