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Related Experiment Video

Updated: Jun 25, 2026

Improving the Success Rate of Protein Crystallization by Random Microseed Matrix Screening

Improving the Success Rate of Protein Crystallization by Random Microseed Matrix Screening

Published on: August 31, 2013

Crystallizing short-read assemblies around seeds.

Mohammad Sajjad Hossain¹, Navid Azimi, Steven Skiena

¹Department of Computer Science, Stony Brook University, Stony Brook, NY 11794-4400 USA. sajjad@cs.sunysb.edu

BMC Bioinformatics

|February 12, 2009

Summary

This summary is machine-generated.

We developed SHORTY, a novel de novo assembler for short-read sequencing data, particularly for the ABI SOLiD platform. SHORTY achieves effective assemblies using paired-end reads and seed sequences, outperforming existing assemblers.

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Area of Science:

Genomics
Bioinformatics

Background:

New short-read sequencing technologies generate massive volumes of 25-30 base paired-end reads.
These reads necessitate different assembly approaches compared to Sanger sequencing and previous assemblers.

Purpose of the Study:

To present a novel short-read de novo assembler, SHORTY, specifically designed for the ABI SOLiD sequencing technology.

Main Methods:

SHORTY utilizes a small number of long seeds (300-500 bp) to augment short paired-end reads.
The assembler employs two key strategies: using single seed reads for assembly crystallization and estimating intercontig distances from multiple spanning paired-end reads.

Main Results:

Demonstrated effective de novo assemblies with N50 contig sizes of approximately 40 kb for three bacterial species using simulated SOLiD data.
Achieved significant assemblies with less than 100x short-read coverage, obtainable in a single sequencer run.

Conclusions:

Sequencing artifacts impacted performance on real data, but results were superior to competing assemblers.
The study presents the first de novo sequence assembly results on real data from the ABI SOLiD platform.