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Technology overview

The technology in this site makes use of a different approach than BLAST technologies. The idea is to use an index sensitive to mutations to find likely matches and then performing a typical local alignment algorithm for the match candidates. It doesn't use a heuristic approach, but in some cases the searches are capped for sub-sequences which have multiple appearences.

Some cases in which it apparently performs better than BLAST:

Query search:

GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCCAACACGGTGA (ALU sub-sequence)

Best result found by BLASTN in chromosome 1 of mouse:

GGCCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGA
Best result found by algorithm in this page in chromosome 1 of mouse:
GCCGGGCGGTGGTGGCTCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCAAGGCCAGCCTGGTCTACAGAGTGA

Alignment of the three sequences:

GGCCGGGC-G-CGGTGGCTCACGCC-TGTAATCCCAGCACTTTGGGAGGC-CGAGGC-GGGCGGA--TC-ACGAG-GTCAGGAGATCGAGACCA-TCCTGG-C-CAACACG-GTGA
G-CCGGGCGGT-GGTGGCTCACGCCTT-TAATCCCAGCACTT-GGGAGGCA-GAGGCAGG-CGGATTTCT--GAGT-TCA--AG---G---CCAG-CCTGGTCT-A-CA-GAGTGA
GGCCGGGC-G-TGGTGGCGCACGCC-TTTAATCCCAGCAC-TTGGGAGGC-AGAGGC-AGGCGGA--T---------TTCTGAGTTCGAGGCCA-GCCTGG-T-CTACAAA-GTGA

Clearly the result found by the algorithm in this page is better. Indeed, it finds a few additional better results for that query.

Query search:

GCCGGGCATGGTGGCGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACANAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAAAAAAAAA (B1 SINE sequence) 

Best results found by BLASTN in the genome of the dog:

TGGTGGCGCACACCTTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGGAT (cr20 range: 5459756-5459808)
GCTGGGCATGGTGGCACATGCCTGTAGTCCTACTAGCTACTTGGGAGGCTGAGGCAGGAGGAT (cr30 range: 18397160-8397222)
Best result found by the algorithm in this page in the genome of the dog (corresponds to the second match found by BLAST):
GCTGGGCATGGTGGCACATGCCTGTAGTCCTACTAGCTACTTGGGAGGCTGAGGCAGGAGGATCGCTTGAGTCCAGGAGTTTGGGGCTGTAGTGGACTATGCTGATAGGATGTCCACACTAAGTCCGGTATCAATATGGTGACCTCCTGGGAGCAGGAGACCACCA (cr30 range: 18397160-18397305 score:22)
Another result found by the algorithm in this page (which corresponds to the best match found by BLAST) but not in the top list of best results when considering the full sequence surrounding it:
CACTGTGGTGGCGCACACCTTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGGATCACTTGAGTCCAGGAGTTCTGGGCTGTACTGCGCTATGCCAAT (cr20-reverse range: 5459713-5459814 score:-3)

Turns out that the algorithm in this page is better suited for finding sequences for phylogenetic trees as it finds sequences with similar sizes which are better to be aligned and compared. Indeed it finds dozens of better alignments than the one presented as the best match by BLAST. Of course it can be argued that BLAST is designed to find the best partial matches, not the best matching sequences to the query sequence, but the point is that this algorithm actually seems to provide a functionality not trivially available with actual BLAST tools.

Query search:
BRCA2 human gene

Best results found by BLASTN in the genome of the chimpanzee:
Chromosome 13 Range: 13386740 to 13413300
Chromosome 9 Range: 109512074 to 109513130
Chromosome 15 Range: 29133481 to 29134527
Best result (the official homolog) found by the algorithm in this page in the chromosome 13 of the chimpanzee
Another result found by the algorithm in this page in the chromosome 7 of the chimpanzee

Whith this algorithm we have found a sequence quite similar to the sequence of the BRCA2 gene. Then, we can find the homolog sequence in the human genome and compare how these two similar sequences have evolved independently considering that one of them is subject to selective pressure and the other one most likely not.
We would not have found that sequence using BLAST as it returns shorter matches.