In addition to the queries by keywords, this data can be queried by sequences (the examples are given in the Application section).
The sequence assemblies can be queried by BLAST at http://jekely-lab.tuebingen.mpg.de/blast/.
Basically, input sequences were queried by BLAST-X against the GenBank non-redundant sequences and ESTs database at the National Center for Biotechnology Information (NCBI) database, taking similarities with an E-value < 10−3 as significant matches.
A single sequence is queried by a group of 8 to 16 probe pairs that constitute a probe set.
All sequences were queried for their similarity to known sequences by use of a BLASTX algorithm [ 64] against the "nr" protein database.
Such sites were found in 7 genes: SFRS11, SFRS1, FMNl2, LEPROT, NICN1, FHOD2, f3-contactin; if one is interested, the binding sites can be searched by sequence (Query 6 in Additional File 1, Section S1.4).
Further, while it is the case that ENU-induced variants are usually found in sequences queried by exome analysis, this may not always be true, and having the entire cohort of novel variants in a recombinant interval may be useful.
A query protein sequence will firstly be processed by the sequence alignment-based predictor.
INDUS algorithm was validated by querying test sequences (constituting four simulated test data sets) against a reference database that was appropriately 'modified' to simulate realistic metagenomic scenarios.
An outgroup dataset was constructed by querying three sequences, UniProt IDs: LICH_BACSU, AGAL_THEMA, and ASPD_THEMA, against the SwissProt database using BLASTP.
