Description: SynaBlast™ (1.0.3) is a nucleotide/protein sequence searching and alignment application that searches the SynaBASE™ database platform and presents results in a BLAST-like output. By leveraging the exhaustive pattern structure of SynaBASE, very significant improvements in sensitivity and performance are observed whilst presenting the results in a familiar interface for online analysis.
Application Example: The protein encoded by the TGIF (TGFB-induced factor) is a member of the three-amino acid loop extension (TALE) superclass of atypical homeodomains, which are highly conserved transcription regulators. Mutations in this gene are associated with holoprosencephaly type 4, a structural defect of the developing forebrain in humans. In this example, we will use the TGIF transcript variant 8 (an alternatively spliced version of which there are 8 in total) to map its position to the human genome (NCBI36) and deduce its exon positions. Using a 1.5Kbp query, SynaBlast was able to search a 3 billion bp SynaBASE in less than ¼ of a second.
To run the example above please:
  1. Go to www.mgrc.com.my.
  2. Click on “SynaBlast”.
  3. Click on “Test Sequence” and select the Newsbyte test sequence labelled “Homo sapiens TGFB-induced factor transcript variant 8” by clicking on the “Copy” button next to the sequence.
  4. The “Homo sapiens genome (NCBI build36 v1)” SynaBASE should be selected.
  5. Using the default parameters given, click on “SynaBlast” to begin your analysis.
Figure 1: The query submission page of SynaBlast (1.0.3).
Figure 2: SynaBlast results page showing the top ranking result mapping to chromosome 18.
Test Sequence

>gi|28178856|ref|NM_174886.1| Homo sapiens TGFB-induced factor (TALE family homeobox) (TGIF),
transcript variant 8, mRNA
CAAAGGCCAGGCCTGACGGAAGAGCCCAGCCTTCGCCGAGGGCCGCAGGGAGCCAGAGACTCGAGCCTGCGGTTCCAG
CCCCGCCGCGGTTCCGGCCCCGCCGCGATCCCGAGGCCTGCGCATGCTCGGTGCTGCGCGGGGCTCCCTCCTTACCGC
AGGAGCTCCTCATCGAGAAACCCAGGTTGGTGTCTTTTCCACGTGGTAGAAGCTGGCTAACCTCCACTTCCACATTCC
AGCCCAAGGGAAAGTCCAAGGTATTGTTGCAGCATCTGGCAGTGAGACTGAGGATGAGGACAGCATGGACATTCCCTT
GGACCTTTCTTCATCCGCTGGCTCAGGCAAGAGAAGGAGAAGGGGCAACCTACCCAAGGAGTCTGTGCAGATTCTTCG
GGATTGGCTGTATGAGCACCGTTACAATGCCTATCCTTCAGAGCAAGAAAAAGCGTTGCTGTCCCAGCAAACACACCT
GTCTACGCTACAGGTCTGTAACTGGTTCATCAACGCCCGCCGCAGGCTCCTCCCTGACATGCTGAGAAAGGATGGCAA
AGATCCAAATCAGTTCACAATTTCCCGCCGTGGGGCCAAGATTTCTGAAACGAGCTCTGTGGAGTCCGTGATGGGCAT
CAAAAACTTCATGCCAGCTCTAGAGGAGACCCCATTTCATTCCTGTACAGCTGGGCCAAACCCAACCCTAGGGAGGCC
ACTGTCTCCTAAGCCGTCATCCCCGGGATCAGTTTTGGCTCGTCCATCAGTGATCTGCCATACCACTGTGACTGCATT
GAAAGATGTCCCTTTCTCTCTCTGCCAGTCGGTCGGTGTGGGACAAAACACAGATATACAGCAGATAGCGGCCAAAAA
CTTCACAGACACCTCTCTCATGTACCCAGAGGACACTTGTAAATCTGGACCAAGTACGAATACACAGAGTGGTCTTTT
CAACACTCCTCCCCCTACTCCACCGGACCTCAACCAGGACTTCAGTGGATTTCAGCTTCTAGTGGATGTTGCACTCAA
ACGGGCTGCAGAGATGGAGCTTCAGGCAAAACTTACAGCTTAACCCATTTTCAAGCAAAACAGTTCTCAGAAATGTCA
TGATTGCCGGGGTGAAGGCAAGAGATGAATTGCATTATTTTATATATTTTTTATTAATATTTGCACATGGGATTGCTA
AAACAGCTTCCTGTTACTGAGATGTCTTCAATGGAATACAGTCATTCCAAGAACTATAAACTTAAAGCTACTGTAGAA
ACAAAGGGTTTTCTTTTTTAAATGTTTCTTGGTAGATTATTCATAATGTGAGATGGTTCCCAATATCATGTGATTTTT
TTTTTCCTCCCCTTCCCTTTTTTTGTTATTTTTTCAGACTGTGCAATACTTAGAGAACCTATAGCATCTTCTCATTCC
CATGTGGAACAGGATGCCCACATACTGTCTAATTAATAAATTTTCCATTTTTTTTCAAACAAGTATGAATCTAGTTGG
TTGATGCCTTTTTTTTCATGACATAATAAAGTATTTTCTTTAAAAAAAAAAAAAAAAA

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