basic local alignment search tool macvector

Strongly hydrophilic areas on the protein surface should be avoided, as well as the destruction of intramolecular contacts in α-helices or β-sheets caused by choosing cloning borders incorrectly. These items of information are necessary for plotting length and mutation planning. Sequence alignments of any protein of interest with any related proteins with a known structure can help to predict secondary structure elements: hydrophobic and hydrophilic parts of the protein surface or stabilizing disulfide bonds. Schnapp, in Comprehensive Medicinal Chemistry II, 2007 3.19.3.2 Sequence Alignments and Analysis To make sure that bcftools has been installed and added into the PATH environmental variable in your Linux environment. To make sure that samtools has been installed and added into the PATH environmental variable in your Linux environment.īCFTools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its Binary Call Format (BCF) counterpart. SAMTools is a tool box with multiple programs for manipulating alignments in the SAM format, including sorting, merging, indexing, and generating alignments in a per-position format.

The SAM format has become the de facto standard format for storing large alignment results because there are several advantages: it is easy to understand, flexible enough to store various types of alignment information, and compact in size. The Sequence Alignment/Map (SAM) format is a generic format for storing large nucleotide sequence alignments.

Yun Zheng, in Computational Non-coding RNA Biology, 2019 1.3.10 SAMTools and BCFTools

Basic local alignment search tool macvector