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unknown title

by Andrey O. Kislyuk, Lee S. Katz, Sonia Agrawal, Matthew S. Hagen, Andrew B. Conley, Pushkala Jayaraman, Viswateja Nelakuditi, Jay C. Humphrey, Scott A. Sammons, Dhwani Govil, Raydel D. Mair, Kathleen M. Tatti, Maria L. Tondella, Brian H. Harcourt, Leonard W. Mayer, I. King Jordan, Alex Bateman
"... A computational genomics pipeline for prokaryotic sequencing projects ..."
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A computational genomics pipeline for prokaryotic sequencing projects

Identification of Prokaryotic and Eukaryotic Signal Peptides and Prediction of Their Cleavage Sites

by Henrik Nielsen, Jacob Engelbrecht, Søren Brunak, Gunnar von Heijne , 1997
"... We have developed a new method for identification of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequences. The method performs significantly better than previous prediction schemes, and can easily be applied on genome-wide ..."
Abstract - Cited by 787 (17 self) - Add to MetaCart
We have developed a new method for identification of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequences. The method performs significantly better than previous prediction schemes, and can easily be applied on genome

Protein structure prediction and structural genomics

by David Baker, Andrej Sali - Science , 2001
"... Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although experimental structure determination methods are providing high-resolution structure information abou ..."
Abstract - Cited by 332 (14 self) - Add to MetaCart
Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although experimental structure determination methods are providing high-resolution structure information

Finding motifs using random projections

by Jeremy Buhler, Martin Tompa , 2001
"... Pevzner and Sze [23] considered a precise version of the motif discovery problem and simultaneously issued an algorithmic challenge: find a motif Å of length 15, where each planted instance differs from Å in 4 positions. Whereas previous algorithms all failed to solve this (15,4)-motif problem, Pevz ..."
Abstract - Cited by 285 (6 self) - Add to MetaCart
, Pevzner and Sze introduced algorithms that succeeded. However, their algorithms failed to solve the considerably more difficult (14,4)-, (16,5)-, and (18,6)motif problems. We introduce a novel motif discovery algorithm based on the use of random projections of the input’s substrings. Experiments

MIPS: analysis and annotation of proteins from whole genomes

by H. W. Mewes, D. Frishman, K. F. X. Mayer, M. Münsterkötter, O. Noubibou, T. Rattei, M. Oesterheld, V. Stümpflen - Nucleic Acids Res , 2004
"... resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of.400 genomes automatically annotated w ..."
Abstract - Cited by 206 (14 self) - Add to MetaCart
resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of.400 genomes automatically annotated

Fast algorithms for large-scale genome alignment and comparison

by Arthur L Delcher , Adam Phillippy , Jane Carlton , Steven L Salzberg - Nucleic Acids Res , 2002
"... ABSTRACT We describe a suffix-tree algorithm that can align the entire genome sequences of eukaryotic and prokaryotic organisms with minimal use of computer time and memory. The new system, MUMmer 2, runs three times faster while using one-third as much memory as the original MUMmer system. It has ..."
Abstract - Cited by 180 (3 self) - Add to MetaCart
ABSTRACT We describe a suffix-tree algorithm that can align the entire genome sequences of eukaryotic and prokaryotic organisms with minimal use of computer time and memory. The new system, MUMmer 2, runs three times faster while using one-third as much memory as the original MUMmer system. It has

The NCBI Prokaryotic Genomes Automatic Annotation Pipeline

by Yiren Yang, Xuefei Yu, Ren Zhang
"... We report the 4.97-Mb draft genome sequence of a highly efficient arsenate-resistant bacterium,Ochrobactrum sp. strain CDB2. It contains a novel arsenic resistance (ars) operon (arsR-arsC1-ACR3-arsC2-arsH-mfs) and two non-operon-associated ars genes, arsC3 and arsB. The genome information will aid i ..."
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We report the 4.97-Mb draft genome sequence of a highly efficient arsenate-resistant bacterium,Ochrobactrum sp. strain CDB2. It contains a novel arsenic resistance (ars) operon (arsR-arsC1-ACR3-arsC2-arsH-mfs) and two non-operon-associated ars genes, arsC3 and arsB. The genome information will aid

Conference Review Computational comparative genomics of eu- and prokaryotes

by Clemens Suter-crazzolara, Günther Kurapkat , 2002
"... With the rapid advent of worldwide genome projects, scientists are confronted with a tremendous increase in the amount of novel information. However, the gap between data collection and interpretation is also growing. For this reason, genome databases contain a wealth of information which is accessi ..."
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With the rapid advent of worldwide genome projects, scientists are confronted with a tremendous increase in the amount of novel information. However, the gap between data collection and interpretation is also growing. For this reason, genome databases contain a wealth of information which

PGAP: pan-genomes analysis pipeline

by Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jingfa Xiao - Bioinformatics
"... Summary: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed. We ..."
Abstract - Cited by 18 (2 self) - Add to MetaCart
Summary: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed

Computational Methods for the Identification of Genes in Vertebrate Genomic Sequences

by Jean-michel Claverie - Hum. Mol. Genet , 1997
"... Research into new methods to identify genes in anonymous genomic sequences has been going on for more than 15 years. Over this period of time, the field has evolved from the designing of programs to identify protein coding regions in compact mitochondrial or bacterial genomes, to the challenge of pr ..."
Abstract - Cited by 67 (3 self) - Add to MetaCart
are still unreliable. As the human and mouse genome sequencing projects enter a production mode, the fully automated annotation of megabase-long anonymous genomic sequences is the next big challenge in bioinformatics.
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