Results 361 to 370 of about 4,504,319 (408)

Aligning a DNA sequence with a protein sequence

Proceedings of the first annual international conference on Computational molecular biology - RECOMB '97, 1997
We develop several algorithms for the problem of aligning DNA sequence with a protein sequence. Our methods account for frameshift errors, but not for introns in the DNA sequence. Thus, they are particularly appropriate for comparing a cDNA sequence that suffers from sequencing errors with an amino acid sequence or a protein sequence database.
Zheng Zhang, William R. Pearson, Webb Miller   +2 more
openaire   +3 more sources

Multiple Sequence Alignment

2008
Multiple sequence alignment (MSA) has assumed a key role in comparative structure and function analysis of biological sequences. It often leads to fundamental biological insight into sequence-structure-function relationships of nucleotide or protein sequence families.
Pirovano, W., Heringa, J.
openaire   +3 more sources

Aligning Sequences to Structures

2007
Most newly sequenced proteins are likely to adopt a similar structure to one which has already been experimentally determined. For this reason, the most successful approaches to protein structure prediction have been template-based methods. Such prediction methods attempt to identify and model the folds of unknown structures by aligning the target ...
openaire   +3 more sources

On global sequence alignment

Bioinformatics, 1994
We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time.
openaire   +3 more sources

RAPID: A ReRAM Processing in-Memory Architecture for DNA Sequence Alignment

International Symposium on Low Power Electronics and Design, 2019
Sequence alignment is a core component of many biological applications. As the advancement in sequencing technologies produces a tremendous amount of data on an hourly basis, this alignment is becoming the critical bottleneck in bioinformatics analysis ...
Saransh Gupta, M. Imani, Behnam Khaleghi, Venkatesh Kumar, Tajana Šimunić   +4 more
semanticscholar   +1 more source

Consistency of optimal sequence alignments [PDF]

Bulletin of Mathematical Biology, 1990
Pairwise optimal alignments between three or more sequences are not necessarily consistent as a whole, but consistent and inconsistent residues are usually distributed in clusters. An efficient method has been developed for locating consistent regions when each pairwise alignment is given in the form of a "skeletal representation" (Bull. math. Biol. 52,
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Sequence Alignment

2022
This chapter focuses on comparing sequences using alignment. Sequence alignment is the operation that consists of matching two or more sequences, in order to highlight their similarity, whether it is local or global. If the alignment is given, then computing a score is a relatively simple task.
openaire   +2 more sources

Sequence Alignment with Tandem Duplication

Journal of Computational Biology, 1997
Algorithm development for comparing and aligning biological sequences has, until recently, been based on the SI model of mutational events which assumes that modification of sequences proceeds through any of the operations of substitution, insertion or deletion (the latter two collectively termed indels). While this model has worked fairly well, it has
openaire   +4 more sources

Malware Sequence Alignment

2016 IEEE International Conferences on Big Data and Cloud Computing (BDCloud), Social Computing and Networking (SocialCom), Sustainable Computing and Communications (SustainCom) (BDCloud-SocialCom-SustainCom), 2016
Sequence alignment has been used to align DNA sequences to find matching segments of DNA from different specimens. Just as DNA sequences can be used to find similar patterns in DNA, this process can also be used on computer programs to identify when segments of code have been reused.
Andrew Dinh, Yaohang Li, Wu He, Daniel Brill   +3 more
openaire   +2 more sources

Sequence Alignment and Homology Search with BLAST and ClustalW.

Cold Spring Harbor Protocols, 2016
This protocol illustrates the steps of searching a sequence database with BLAST, which in essence performs pairwise alignment between the query sequence and each target sequence in the database.
Jui-Hung Hung, Z. Weng
semanticscholar   +1 more source