**Sequence Analysis**

74 Bioinformatics

207.

[57] Ideker T, Ozier O, Schwikowski B, Siegel AF (2002) Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 18:S233–S240. [58] Maxfield L, Fraize C, Coffin JM (2005) Relationship between retroviral DNAintegrationsite selection and host cell transcription. Proc natl acad.sci. 102 (5):1436–1441. [59] Schroder AR, Shinn P, Chen H, Berry C, Ecker JR, Bushman F (2002) HIV-1 integration in the human genome favors active genes and local hotspots. Cell. 110 (4):521–529. [60] Dérijard B, Hibi M, Wu IH, Barrett T, Su B, Deng T, Karin M, Davis RJ (1994) JNK1: a protein kinase stimulated by UV light and Ha-Ras that binds and phosphorylates the c-

[61] Mordret G, (1993) MAP kinase: a node connecting multiple pathways. Biol. cell. 79:193–

[64] Chugh P, Bradel-Tretheway B, Monteiro-Filho CM, Planelles V, Maggirwar SB, Dewhurst S, Kim B (2008) Akt inhibitors as an HIV-1 infected macrophagespecific anti-

[62] Rao KM, (2001) MAP kinase activation in macrophages. J. Leukoc. Biol. 69 (1):3–10. [63] Osaki M, Oshimura M, Ito M ( 2004) PI3K-Akt pathway: its functions and alterations in

Jun activation domain. Cell. 76:1025–1037.

human cancer. Apoptosis. 9 (6):667–676.

viral therapy. Retrovirology. 5:11.

**Chapter 4** 

© 2012 Zwick et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

© 2012 Zwick et al., licensee InTech. This is a paper distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

**SeqAnt 2012: Recent Developments in** 

Matthew Ezewudo, Promita Bose, Kajari Mondal, Viren Patel,

Dhanya Ramachandran and Michael E. Zwick

Additional information is available at the end of the chapter

http://dx.doi.org/10.5772/53339

**1. Introduction** 

genomics technologies.

variation.

**Next-Generation Sequencing Annotation** 

The discovery of genome-wide genetic variation was central to the field of genomics [1,2]. Now, recent advances in second-generation sequencing technologies and better methods of targeted enrichment mean the detection of genome-wide patterns of genetic variation will soon be a routine operation [3,4]. Yet these advances in DNA sequencing have revealed a new bottleneck: the functional classification and interpretation of newly discovered genetic

The scale of this problem is enormous. The high throughput and low cost of secondgeneration sequencing platforms now allow geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites in a single individual, but the methods that exist to annotate these variant sites using information from publicly available databases are too slow to be useful for the large sequencing datasets being generated. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to annotate variant sites efficiently can be a major bottleneck in genetics research and clinical applications of

To address this problem, we developed the Sequence Annotator (SeqAnt, http://seqant.genetics.emory.edu/), an open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing experiments [5]. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation. Annotated variants can be viewed on a web browser, downloaded in a tabdelimited text file, or directly uploaded in a Browser Extensible Document (BED) format to the UCSC Genome Browser. To demonstrate the speed of SeqAnt, we annotated a series of

**Chapter 4** 
