SEQUENCE ALIGNMENT TOOLSJackson, Benjamin NAluru, Srinivas
Tools for the Simulation and Detection of Coevolving Positions in Multiple Sequence Alignments 来自 Semantic Scholar 喜欢 0 阅读量: 19 作者: Domenico L. Gatti 摘要: In the multiple sequence alignment (MSA) of the members of a protein family some positions are highly conserved, while others vary...
“DNASTAR is my favorite tool for sequence analysis. My colleagues also love it.” Dr. Xin Yin, Sanford Burnham Prebys Medical Discovery Institute “Easy to use, intuitive interface makes working with sequences easy.” Matthew Nilles, University of North Dakota ...
Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generati...
Comprehensive suite of molecular biology and bioinformatics tools for protein, Sanger and next generation sequencing analysis
The complexity measures for amino acid sequences could be calculated by the same entropy and compression-based algorithms. But the functional and evolutionary roles of low complexity regions in protein have specific features differing from DNA. The tools for protein sequence complexity aimed for ...
#GFA outputvg view x.vg>x.gfa#dot output suitable for graphvizvg view -d x.vg>x.dot#And if you have a GAM filecp small/x-s1337-n1.gam x.gam#json version of binary alignmentsvg view -a x.gam>x.json Mapping If you have more than one sequence, or you are working on a large...
(E-value, BitScore, etc.), and the sequence alignment between the conserved domain and the query sequence can be returned. In order to run the rpsbproc utility, the output file generated by RPS-BLAST executables needs to be stored in ASN.1 format, using “.asn” as the filename ...
Finally, a sequence alignment depends on multiple a priori assumptions about the evolution of the sequences that are being compared. These various parameters (e.g., substitution matrices, gap penalties, and threshold values for statistical parameters) are somewhat arbitrary, which additionally strains ...
Biopython provides tools for working with DNA, RNA, and protein sequences, includingsequence alignment, motif and pattern matching, and translation between nucleotide and protein sequences. Biopython includes tools for working with protein structures, such as parsing and manipulating PDB files and perfor...