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» Extending assembly of short DNA sequences to handle error
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BMCBI
2006
100views more  BMCBI 2006»
13 years 4 months ago
DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions
Background: Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not ...
Erik Arner, Martti T. Tammi, Anh-Nhi Tran, Ellen K...
EDBT
2010
ACM
117views Database» more  EDBT 2010»
13 years 11 months ago
Anchoring millions of distinct reads on the human genome within seconds
With the advent of next-generation DNA sequencing machines, there is an increasing need for the development of computational tools that can anchor accurately and expediently the m...
Tien Huynh, Michail Vlachos, Isidore Rigoutsos
BMCBI
2006
99views more  BMCBI 2006»
13 years 4 months ago
MAGIC-SPP: a database-driven DNA sequence processing package with associated management tools
Background: Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA seque...
Chun Liang, Feng Sun, Haiming Wang, Junfeng Qu, Ro...
BMCBI
2007
106views more  BMCBI 2007»
13 years 4 months ago
Simultaneous identification of long similar substrings in large sets of sequences
Background: Sequence comparison faces new challenges today, with many complete genomes and large libraries of transcripts known. Gene annotation pipelines match these sequences in...
Jürgen Kleffe, Friedrich Möller, Burghar...
BMCBI
2007
109views more  BMCBI 2007»
13 years 4 months ago
Discarding duplicate ditags in LongSAGE analysis may introduce significant error
Background: During gene expression analysis by Serial Analysis of Gene Expression (SAGE), duplicate ditags are routinely removed from the data analysis, because they are suspected...
Jeppe Emmersen, Anna M. Heidenblut, Annabeth Laurs...