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base sequence

Overview page. Subjects: Chemistry — Psychology.

Another name for a DNA sequence. [So called because it is made up of bases]

See overview in Oxford Index

complementary base sequence

Edited by Richard Cammack, Teresa Atwood, Peter Campbell, Howard Parish, Anthony Smith, Frank Vella and John Stirling.

in Oxford Dictionary of Biochemistry and Molecular Biology

January 2006; p ublished online January 2008 .

Reference Entry. Subjects: Biochemistry. 29 words.

a sequence in a polynucleotide chain in which all the bases are able to form base pairs with a sequence

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complementary base sequence

Robert C. King, William D. Stansfield and Pamela K. Mulligan.

in A Dictionary of Genetics

January 2007; p ublished online January 2007 .

Reference Entry. Subjects: Genetics and Genomics. 40 words.

a sequence of polynucleotides related by the base-pairing rules. For example, in DNA a sequence A-G-T in one strand is

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complementary base sequence

Robert C. King, Pamela K. Mulligan and William D. Stansfield.

in A Dictionary of Genetics

January 2013; p ublished online January 2014 .

Reference Entry. Subjects: Genetics and Genomics. 40 words.

a sequence of polynucleotides related by the base-pairing rules. For example, in DNA a sequence A-G-T in one strand is

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complementary base sequence

Overview page. Subjects: Genetics and Genomics — Chemistry.

A sequence of polynucleotides related by the base-pairing rules. For example, in DNA a sequence A-G-T in one strand is complementary to T-C-A in the other strand. A given sequence defines...

See overview in Oxford Index

Contact‐based sequence alignment

Jens Kleinjung, John Romein, Kuang Lin and Jaap Heringa.

in Nucleic Acids Research

April 2004; p ublished online April 2004 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5535 words.

This paper introduces the novel method of contact‐based protein sequence alignment, where structural information in the form of contact mutation probabilities is incorporated into an...

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The Genome Sequence DataBase

C. Harger, G. Chen, A. Farmer, W. Huang, J. Inman, D. Kiphart, F. Schilkey, M. P. Skupski and J. Weller.

in Nucleic Acids Research

January 2000; p ublished online January 2000 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 1535 words.

The Genome Sequence DataBase (GSDB) is a database of publicly available nucleotide sequences and their associated biological and bibliographic information. Several notable changes have...

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Segment-based multiple sequence alignment

Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cedric Notredame and Knut Reinert.

in Bioinformatics

August 2008; p ublished online August 2008 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 5016 words.

Motivation: Many multiple sequence alignment tools have been developed in the past, progressing either in speed or alignment accuracy. Given the importance and wide-spread use...

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Accurate sequence-based prediction of catalytic residues

Tuo Zhang, Hua Zhang, Ke Chen, Shiyi Shen, Jishou Ruan and Lukasz Kurgan.

in Bioinformatics

October 2008; p ublished online August 2008 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 8442 words.

Motivation: Prediction of catalytic residues provides useful information for the research on function of enzymes. Most of the existing prediction methods are based on...

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Local RNA base pairing probabilities in large sequences

Stephan H. Bernhart, Ivo L. Hofacker and Peter F. Stadler.

in Bioinformatics

March 2006; p ublished online December 2005 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1090 words.

Summary: The genome-wide search for non-coding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative...

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Model-based prediction of sequence alignment quality

Virpi Ahola, Tero Aittokallio, Mauno Vihinen and Esa Uusipaikka.

in Bioinformatics

October 2008; p ublished online August 2008 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 6158 words.

Motivation: Multiple sequence alignment (MSA) is an essential prerequisite for many sequence analysis methods and valuable tool itself for describing relationships between...

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Ligase-based detection of mononucleotide repeat sequences

Monib Zirvi, Francis Barany, Takamori Nakayama, Gregg Newman, Timothy McCaffrey and Philip Paty.

in Nucleic Acids Research

December 1999; p ublished online December 1999 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 4468 words.

Up to 15% of all colorectal cancers are considered to be replication error positive (RER+) and contain mutations at hundreds of thousands of microsatellite repeat sequences. Recently, a...

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Incremental window-based protein sequence alignment algorithms

Huzefa Rangwala and George Karypis.

in Bioinformatics

January 2007; p ublished online January 2007 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 4985 words.

Motivation: Protein sequence alignment plays a critical role in computational biology as it is an integral part in many analysis tasks designed to solve problems in comparative...

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SBSPKS: structure based sequence analysis of polyketide synthases

Swadha Anand, M. V. R. Prasad, Gitanjali Yadav, Narendra Kumar, Jyoti Shehara, Md. Zeeshan Ansari and Debasisa Mohanty.

in Nucleic Acids Research

July 2010; p ublished online May 2010 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 6522 words.

Polyketide synthases (PKSs) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. Bioinformatics analysis of sequence and structural features of PKS...

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Protein solubility: sequence based prediction and experimental verification

Pawel Smialowski, Antonio J. Martin-Galiano, Aleksandra Mikolajka, Tobias Girschick, Tad A. Holak and Dmitrij Frishman.

in Bioinformatics

October 2007; p ublished online December 2006 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 6453 words.

Motivation: Obtaining soluble proteins in sufficient concentrations is a recurring limiting factor in various experimental studies. Solubility is an individual trait of...

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Sequence-based prediction of protein domains

Jinfeng Liu and Burkhard Rost.

in Nucleic Acids Research

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 7272 words.

Guessing the boundaries of structural domains has been an important and challenging problem in experimental and computational structural biology. Predictions were based on intuition,...

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base sequence

Overview page. Subjects: Chemistry — Psychology.

Another name for a DNA sequence. [So called because it is made up of bases]

See overview in Oxford Index

base sequence

Edited by Richard Cammack, Teresa Atwood, Peter Campbell, Howard Parish, Anthony Smith, Frank Vella and John Stirling.

in Oxford Dictionary of Biochemistry and Molecular Biology

January 2006; p ublished online January 2008 .

Reference Entry. Subjects: Biochemistry. 15 words.

the sequential order of nucleotide residues in a polynucleotide or nucleic acid molecule.

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Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

Ivan Borozan, Stuart Watt and Vincent Ferretti.

in Bioinformatics

May 2015; p ublished online January 2015 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 7292 words.

Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally...

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ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences

Byungwook Lee, Taehui Hong, Sang Jin Byun, Taeha Woo and Yoon Jeong Choi.

in Nucleic Acids Research

July 2007; p ublished online July 2007 .

Journal Article. Subjects: Chemistry; Biochemistry; Bioinformatics and Computational Biology; Genetics and Genomics; Molecular and Cell Biology. 2237 words.

We present a web-based server, called ESTpass, for processing and annotating sequence data from expressed sequence tag (EST) projects. ESTpass accepts a FASTA-formatted EST file and its...

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CREDO: a web-based tool for computational detection of conserved sequence motifs in noncoding sequences

Tobias Hindemitt and Klaus F. X. Mayer.

in Bioinformatics

P ublished online October 2005 .

Journal Article. Subjects: Bioinformatics and Computational Biology. 1263 words.

Summary: CREDO is a user-friendly, web-based tool that integrates the analysis and results of different algorithms widely used for the computational detection of conserved...

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