Description:
SynaSearch™ is an application for rapid database searching and alignment of sequence data within SynaBASE. It harnesses the exhaustive dynamic k-mer pattern structure of SynaBASE to rapidly and effectively align sequences.

Application Example:
Transcript variant 1 of the Homo sapiens NLR family apoptosis inhibitory protein (NAIP) gene resides on a 500kb inverted duplication on chromosome 5 (q13). This duplicated region contains at least four other genes and repetitive elements which make it very prone to genomic re-arrangements and deletions. The complexity of the sequence in this region makes it difficult to accurately determine its organisation.

In this example, SynaSearch was used to enable rapid visualisation of the aligned sequences in order to provide an overview of gene organisation within the genome. The NAIP gene used in this example is homologous to two baculovirus apoptosis inhibitor proteins [1,2] (Cp-IAP and Op-IAP). It is partly deleted in individuals with type I SMA (spinal muscular atrophy) which is also caused by mutations in an overlapping neighbouring gene encoding the survival motor neuron, SMN1. The protein encoded by the NAIP gene is able to suppress apoptosis through inhibition of caspases and is induced by various anti-apoptotic (IAP) type signals. One such pathway is through calcium-induced cell death via caspase-3-dependant and caspase-3-independant pathways [3]. In this case, enhanced binding of hippocalcin, a member of neuron specific proteins, to the BIR 1-3 domain of NAIP appears to augment the latter's suppression of apoptosis.

The significance of this inverted duplication within this region of chromosome 5 is still poorly understood. However, by using SynaSearch to align the 6.5Kbp sequence to the human genome an interactive and very informative view of how the query maps to the human genome is observed. By using the viewer it is clearly evident that a region of approximately 5,000bp on the query aligns to other sections of chromosome 5 (q13) which is part of the earlier mentioned duplicated region. These aligned regions belong to other genes that may share the same functional domain(s). For example, based on the graph, the section that aligns to the 69,400,000bp region of chromosome 5 actually belongs to part of a SMN transcript as well as the NAIP pseudogene (RefSeq).

To run the example above, please:

Go to www.mgrc.com.my.
Click on SynaSearch.
Click on Test Sequence and select Application Note test sequence July 2007 by clicking on the "copy" button next to it.
Set the Minimum Match Length to 15.
Set the Repeat Filter to Strong - MRF 1.0
Set the Score to '30'.
Click on the Advance Options panel.
On the Region parameter, input '1075316' (This number, the length of chromosome 5, is used to specify the maximum size of a potential alignment. See Figure 1).
Click on SEARCH.
In the results window, click on the 'Bit Score' of the top most ranked alignment or target to obtain a graphical overview of the alignment (Figure 3).
Click the button on the right to view the actual alignments.

Figure 1:

The input page of SynaSearch (1.2.4) showing the NAIP test sequence in the query box.

Figure 2:

SynaSearch (1.2.4) showing top matching results to human chromosome 5. The link to graphical alignment overview is highlighted in red.

Figure 3:

Graphical overview of SynaSearch alignment for NAIP on human chromosome 5.

References:
1. N E Crook, R J Clem, and L K Miller (1993) An apoptosis-inhibiting baculovirus gene with a zinc finger-like motif J Virol. 67(4): 2168-2174.
2. R J Clem and L K Miller (1994 Control of programmed cell death by the baculovirus genes p35 and iap. Mol Cell Biol. 14(8): 5212-5222.
3. E A Mercer, L Korhonen, Y Skoglosa, P A Olsson, J P Kukkonen and D Lindholm (2000) NAIP interacts with hippocalcin and protects neurons against calcium -induced cell death through caspase -3-dependent and -independent pathways. The EMBO Journal. 19: 3597-3607

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