NDLI: Large scale sequencing by hybridization

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The sequence of the human genome (abstract only)

A new approach to sequence comparison: normalized sequence alignment

Context-specific Bayesian clustering for gene expression data

An optimal procedure for gap closing in whole genome shotgun sequencing

Class discovery in gene expression data

On the predictive power of sequence similarity in yeast

Algorithms for phylogenetic footprinting

Predicting the β-helix fold from protein sequence data

Information processing by cells and biologists (abstract only)

Finding motifs using random projections

Rapid significance estimation in local sequence alignment with gaps

Regulatory element detection using correlation with expression (abstract only)

Gene-finding via tandem mass spectrometry

Algorithms for identifying protein cross-links via tandem mass spectrometry

Hunger for new technologies, metrics, and spatiotemporal models in functional genomic (abstract only)

Fast recovery of evolutionary trees with thousands of nodes

Geometric algorithms for the analysis of 2D-electrophoresis gels

Analysis techniques for microarray time-series data

A structural EM algorithm for phylogenetic inference

Optimal sequencing by hybridization in rounds

Efficient algorithms for lateral gene transfer problems

The greedy path-merging algorithm for sequence assembly

Extracting structural information using time-frequency analysis of protein NMR data

Separating repeats in DNA sequence assembly

A NMR-spectra-based scoring function for protein docking

101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem

Comparative analysis of organelle genomes, a biologist's view of computational challenges (abstract only)

DNA segmentation as a model selection process

Edit distance between two RNA structures

Genetics and genemoics: impact on drug discovery and development

The role of computational chemistry in translating genomic information into bioactive small molecules (abstract only)

Comparing sequence scaffolds

Fast and simple character classes and bounded gaps pattern matching, with application to protein searching

Applications of generalized pair hidden Markov models to alignment and gene finding problems

Gene functional classification from heterogeneous data

A new approach to fragment assembly in DNA sequencing

Imposing specificity by regulated localization (abstract only)

Large scale sequencing by hybridization

RNA biology and the genome (abstract only)

Towards predicting coiled-coil protein interactions

Using motion planning to study protein folding pathways

Zinc finger gene clusters and tandem gene duplication

A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes

Creating the backbone for the virtual cell (abstract only): cell mapping projects on the run

Creating the backbone for the virtual cell: cell mapping projects on the run

Large scale sequencing by hybridization

Content Provider	ACM Digital Library
Author	Tsur, Dekel Shamir, Ron
Abstract	Sequencing by hybridization is a method for reconstructing a DNA sequence based on its k-mer content. This content, called the spectrum of the sequence, can be obtained from hybridization with a universal DNA chip. However, even with a sequencing chip containing all $4^{9}$ 9-mers and assuming no hybridization errors, only about 400 bases-long sequences can be reconstructed unambiguously.Drmanac et al. suggested sequencing long DNA targets by obtaining spectra of many short overlapping fragments of the target, inferring their relative positions along the target and computing spectra of subfragments that are short enough to be uniquely recoverable. Drmanac et al. do not treat the realistic case of errors in the hybridization process. In this paper we study the effect of such errors. We show that the probability of ambiguous reconstruction in the presence of (false negative) errors is close to the probability in the errorless case. More precisely, the ratio between these probabilities is 1 + &Ogr;(p/(1 - $p)^{4}$ · 1/d) where d is the average distance between neighboring subfragments, and p is the probability of a false negative.We also obtain lower and upper bounds for the probability of unambiguous reconstruction based on errorless spectrum. For realistic chip sizes, these bounds are tighter than those given by Arratia et al. Finally, we report results on simulations with real DNA sequences, showing that even in the presence of 50% false negative errors, a target of cosmid length can be recovered with less than 0.1% miscalled bases.
Starting Page	269
Ending Page	277
Page Count	9
File Format	PDF
ISBN	1581133537
DOI	10.1145/369133.369233
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2001-04-22
Publisher Place	New York
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Large Scale Sequencing by Hybridization (2002)

Optimal sequencing by hybridization in rounds

Large scale sequencing by hybridization (2002)

Large scale sequencing by hybridization

Large scale sequencing by hybridization (2002)

Accelerating DNA sequencing-by-hybridization with noise

Sequencing by Hybridization in the Presence of Hybridization Errors

Genome Analysis by Large Scale Sequencing

Handling long targets and errors in sequencing by hybridization

Large scale sequencing by hybridization

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