Notably, probes from such batch-wise query meet the requirements of microarray probe design.
Pair-wise orthologous relationships between the query species and JCM1112 were established by comparing their genome sequences (retrieved in May 2009 from GenBank), resorting to the stand-alone version of Inparanoid (version 3.0) using BLOSUM80 as the substitution matrix [78].
This tool enables researchers to search their queries against sequence databases and produces an output of pair-wise alignments based on the query sequences and matching sequences from the database (referred to as hits).
The user can query for microsatellites, chromosome wise (1 24, X, M and U), where more than one chromosome may be selected at a time from water buffalo genome.
Rather than requiring data scientists to analyze and query big data, a wiser and more efficient way to maximize its benefit is to leave the detection phase to machine learning.
In this section, we describe how our initial query can be step-wise narrowed to a much more specific query that returns only six parts from our knowledgebase.
A pair-wise alignment is computed between the query Q and each candidate parent P.
To be considered an LTR sequence in this study, a BLAST "hit" had to display 60% sequence homology to the LTR query sequence in a pair-wise comparison test [ 43] and have a size 40% of that of the LTR query sequence.
Next we computed the pair wise neural response N (i, j) between the query sequence i and the sequence j (1..n) in the base dataset.
Sometimes, even if the input vector is large, pair-wise ratings between the queried for item and the items in the input vector may not exist, which will reduce the prediction time.
For the similarity search results, pair-wise alignments of the queries with the corresponding hits are shown, but the user also has the possibility to request for a multiple alignment of all the hits using Clustal Omega (54) along with a representation of the residue frequencies at each position produced by WebLogo (55).
