![]() ![]() You could simply simple state the definition of the E-value in the report. Thus the simple answer is to use Blast E-value (bit-score) and it is a universally recognised metric, the reader can then make up their own mind what the value represents. Functional domains within the Blast variant (Blast-Psi) could be of use, its field specific however. for house-keeping genes as a starting point. Protein and gene sequence comparisons are done with BLAST (Basic Local Alignment Search Tool). Identifying homologues would require a phylogenetic tree which is compatible with the established phylogenetic tree, e.g. the selection pressures of convergence could very difference. When trying to assign a function to a amino acid locus this starts becoming relevant because e.g. This is simply because amino acid loci could have arisen by convergent evolution rather than direct descendancy which are homologues and this can become controversial. The broader question concerns the whether the Blast hit is a genuine homology and that is very complicated. COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information. If two multiple sequence alignments of related. BLAST searches can identify similar sequences in different organisms AND BLASTn allows nucleotide sequence alignment while BLASTp allows protein alignment. Using a local blast server will provide a specific query verse reference E-value. When aligning sequences to structures, SALIGN uses structural environment information to place gaps optimally. Thus the smaller the E-value the better the hit. Up to 10 hits can be expected to be found just by chance, given the Enter multiple protein or nucleotide sequences, separated by a FASTA header. (score) that could be found just by chance. Find a protein sequence by UniProt ID (e.g. The BLAST E-value is the number of expected hits of similar quality AlignmentViewer is multiple sequence alignment viewer for protein families with flexible visualization, analysis tools and links to protein family databases. Just formalise the answer, its a straight use of the Blast E-value and I wouldn't personally advise against anything beyond that (explained below) within molecular evolution. ![]()
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