Table of Contents

Editor's Note

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Editor’s Note
- Laurie Goodman
Genome Res. March 1, 1998 8: 159; doi:10.1101/gr.8.3.159

INSIGHT/OUTLOOK

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Base Qualities Help Sequencing Software
- Richard Durbin and
- Simon Dear
Genome Res. March 1, 1998 8: 161-162; doi:10.1101/gr.8.3.161
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Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis
- Jonathan A. Eisen
Genome Res. March 1, 1998 8: 163-167; doi:10.1101/gr.8.3.163
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Late-Night Thoughts on the Sequence Annotation Problem
- Sarah J. Wheelan and
- Mark S. Boguski
Genome Res. March 1, 1998 8: 168-169; doi:10.1101/gr.8.3.168
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WebWise: Guide to the Baylor College of Medicine Human Genome Sequencing Center’s Web Site
- Kim D. Pruitt
Genome Res. March 1, 1998 8: 170-174; doi:10.1101/gr.8.3.170

RESEARCH

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Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment
- Brent Ewing,
- LaDeana Hillier,
- Michael C. Wendl,
- and Phil Green
Genome Res. March 1, 1998 8: 175-185; doi:10.1101/gr.8.3.175
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Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
- Brent Ewing and
- Phil Green
Genome Res. March 1, 1998 8: 186-194; doi:10.1101/gr.8.3.186
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Consed: A Graphical Tool for Sequence Finishing
- David Gordon,
- Chris Abajian,
- and Phil Green
Genome Res. March 1, 1998 8: 195-202; doi:10.1101/gr.8.3.195
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Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome Sequence
- Hidemasa Bono,
- Hiroyuki Ogata,
- Susumu Goto,
- and Minoru Kanehisa
Genome Res. March 1, 1998 8: 203-210; doi:10.1101/gr.8.3.203
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Software for Constructing and Verifying Pedigrees within Large Genealogies and an Application to the Old Order Amish of Lancaster County
- Richa Agarwala,
- Leslie G. Biesecker,
- Katherine A. Hopkins,
- Clair A. Francomano,
- and Alejandro A. Schaffer
Genome Res. March 1, 1998 8: 211-221; doi:10.1101/gr.8.3.211
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Computational Advances in Maximum Likelihood Methods for Molecular Phylogeny
- Eric E. Schadt,
- Janet S. Sinsheimer,
- and Kenneth Lange
Genome Res. March 1, 1998 8: 222-233; doi:10.1101/gr.8.3.222
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GAIA: Framework Annotation of Genomic Sequence
- L. Charles Bailey, Jr.,
- Stephen Fischer,
- Jonathan Schug,
- Jonathan Crabtree,
- Mark Gibson,
- and G. Christian Overton
Genome Res. March 1, 1998 8: 234-250; doi:10.1101/gr.8.3.234

Letters

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Estimation of Errors in “Raw” DNA Sequences: A Validation Study
- Peter Richterich
Genome Res. March 1, 1998 8: 251-259; doi:10.1101/gr.8.3.251
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Sequence Assembly with CAFTOOLS
- Simon Dear,
- Richard Durbin,
- LaDeana Hillier,
- Gabor Marth,
- Jean Thierry-Mieg,
- and Richard Mott
Genome Res. March 1, 1998 8: 260-267; doi:10.1101/gr.8.3.260
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EbEST: An Automated Tool Using Expressed Sequence Tags to Delineate Gene Structure
- Jian Jiang and
- Howard J. Jacob
Genome Res. March 1, 1998 8: 268-275; doi:10.1101/gr.8.3.268
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Alternative Gene Form Discovery and Candidate Gene Selection from Gene Indexing Projects
- John Burke,
- Hui Wang,
- Winston Hide,
- and Daniel B. Davison
Genome Res. March 1, 1998 8: 276-290; doi:10.1101/gr.8.3.276
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BioViews: Java-Based Tools for Genomic Data Visualization
- Gregg A. Helt,
- Suzanna Lewis,
- Ann E. Loraine,
- and Gerald M. Rubin
Genome Res. March 1, 1998 8: 291-305; doi:10.1101/gr.8.3.291
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SeqHelp: A Program to Analyze Molecular Sequences Utilizing Common Computational Resources
- Ming K. Lee,
- Eric D. Lynch,
- and Mary-Claire King
Genome Res. March 1, 1998 8: 306-312; doi:10.1101/gr.8.3.306
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Kaleidaseq: A Web-Based Tool to Monitor Data Flow in a High Throughput Sequencing Facility
- Neilay N. Dedhia and
- W. Richard McCombie
Genome Res. March 1, 1998 8: 313-318; doi:10.1101/gr.8.3.313
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Identification of Human Gene Core Promoters in Silico
- Michael Q. Zhang
Genome Res. March 1, 1998 8: 319-326; doi:10.1101/gr.8.3.319

Editor's Note

Editor’s Note

INSIGHT/OUTLOOK

Base Qualities Help Sequencing Software

Phylogenomics: Improving Functional Predictions for Uncharacterized Genes by Evolutionary Analysis

Late-Night Thoughts on the Sequence Annotation Problem

WebWise: Guide to the Baylor College of Medicine Human Genome Sequencing Center’s Web Site

RESEARCH

Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment

Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities

Consed: A Graphical Tool for Sequence Finishing

Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome Sequence

Software for Constructing and Verifying Pedigrees within Large Genealogies and an Application to the Old Order Amish of Lancaster County

Computational Advances in Maximum Likelihood Methods for Molecular Phylogeny

GAIA: Framework Annotation of Genomic Sequence

Letters

Estimation of Errors in “Raw” DNA Sequences: A Validation Study

Sequence Assembly with CAFTOOLS

EbEST: An Automated Tool Using Expressed Sequence Tags to Delineate Gene Structure

Alternative Gene Form Discovery and Candidate Gene Selection from Gene Indexing Projects

BioViews: Java-Based Tools for Genomic Data Visualization

SeqHelp: A Program to Analyze Molecular Sequences Utilizing Common Computational Resources

Kaleidaseq: A Web-Based Tool to Monitor Data Flow in a High Throughput Sequencing Facility

Identification of Human Gene Core Promoters in Silico

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