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  1. The BLAST algorithm compares biological sequences to one another in order to determine shared motifs and common ancestry. However, the comparison of all non-redundant (NR) sequences against all other NR sequen...

    Authors: Michel Dumontier and Christopher WV Hogue

    Citation: BMC Bioinformatics 2002 3:13

    Content type: Methodology article

    Published on:

  2. Escherichia coli guanine-N2 (m2G) methyltransferases (MTases) RsmC and RsmD modify nucleosides G1207 and G966 of 16S rRNA. They possess a common MTase domain in the C-terminus and a variable region in the N-termi...

    Authors: Janusz M Bujnicki and Leszek Rychlewski

    Citation: BMC Bioinformatics 2002 3:10

    Content type: Research article

    Published on:

  3. Pattern matching is the core of bioinformatics; it is used in database searching, restriction enzyme mapping, and finding open reading frames. It is done repeatedly over increasingly long sequences, thus codes...

    Authors: Harry J Mangalam

    Citation: BMC Bioinformatics 2002 3:8

    Content type: Methodology article

    Published on:

  4. Gene regulation in eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational metho...

    Authors: Michele Caselle, Ferdinando Di Cunto and Paolo Provero

    Citation: BMC Bioinformatics 2002 3:7

    Content type: Methodology article

    Published on:

  5. For over a decade the idea of representing biological sequences in a continuous coordinate space has maintained its appeal but not been fully realized. The basic idea is that any sequence of symbols may define...

    Authors: Jonas S Almeida and Susana Vinga

    Citation: BMC Bioinformatics 2002 3:6

    Content type: Methodology article

    Published on:

  6. Analysis of any newly sequenced bacterial genome starts with the identification of protein-coding genes. Despite the accumulation of multiple complete genome sequences, which provide useful comparisons with cl...

    Authors: Stéphanie Bocs, Antoine Danchin and Claudine Médigue

    Citation: BMC Bioinformatics 2002 3:5

    Content type: Research article

    Published on:

  7. We provide a systematic study of the sources of variability in expression profiling data using 56 RNAs isolated from human muscle biopsies (34 Affymetrix MuscleChip arrays), and 36 murine cell culture and tiss...

    Authors: Marina Bakay, Yi-Wen Chen, Rehannah Borup, Po Zhao, Kanneboyina Nagaraju and Eric P Hoffman

    Citation: BMC Bioinformatics 2002 3:4

    Content type: Research article

    Published on:

  8. Comparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic...

    Authors: Jamie J Cannone, Sankar Subramanian, Murray N Schnare, James R Collett, Lisa M D'Souza, Yushi Du, Brian Feng, Nan Lin, Lakshmi V Madabusi, Kirsten M Müller, Nupur Pande, Zhidi Shang, Nan Yu and Robin R Gutell

    Citation: BMC Bioinformatics 2002 3:2

    Content type: Research article

    Published on:

  9. Most profile and motif databases strive to classify protein sequences into a broad spectrum of protein families. The next step of such database studies should include the development of classification systems ...

    Authors: Kevin Truong and Mitsuhiko Ikura

    Citation: BMC Bioinformatics 2002 3:1

    Content type: Methodology article

    Published on:

  10. Currently, most genome annotation is curated by centralized groups with limited resources. Efforts to share annotations transparently among multiple groups have not yet been satisfactory.

    Authors: Robin D Dowell, Rodney M Jokerst, Allen Day, Sean R Eddy and Lincoln Stein

    Citation: BMC Bioinformatics 2001 2:7

    Content type: Research article

    Published on:

  11. Prediction of protein structures is one of the fundamental challenges in biology today. To fully understand how well different prediction methods perform, it is necessary to use measures that evaluate their pe...

    Authors: Susana Cristobal, Adam Zemla, Daniel Fischer, Leszek Rychlewski and Arne Elofsson

    Citation: BMC Bioinformatics 2001 2:5

    Content type: Research article

    Published on:

  12. Leucine-rich repeats are one of the more common modules found in proteins. The leucine-rich repeat consensus motif is LxxLxLxxNxLxxLxxLxxLxx- where the first 11–12 residues are highly conserved and the remaind...

    Authors: Colin W Ward and Thomas PJ Garrett

    Citation: BMC Bioinformatics 2001 2:4

    Content type: Research article

    Published on:

  13. We apply a new machine learning method, the so-called Support Vector Machine method, to predict the protein structural class. Support Vector Machine method is performed based on the database derived from SCOP,...

    Authors: Yu-Dong Cai, Xiao-Jun Liu, Xue-biao Xu and Guo-Ping Zhou

    Citation: BMC Bioinformatics 2001 2:3

    Content type: Research article

    Published on:

  14. The 5'-terminal cap structure plays an important role in many aspects of mRNA metabolism. Capping enzymes encoded by viruses and pathogenic fungi are attractive targets for specific inhibitors. There is a larg...

    Authors: Janusz M Bujnicki, Marcin Feder, Monika Radlinska and Leszek Rychlewski

    Citation: BMC Bioinformatics 2001 2:2

    Content type: Research article

    Published on:

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