منابع مشابه
A large database DNA sequence handling program with generalized searching specifications
The program described allows for the creation and manipulation of files of DNA sequence data up to very great lengths. The program uses its own paging system to load segments of the sequence into a small internal buffer so that the program does not have excessive memory requirements. The program offers a menu of functions to the user, and has been written to be forgiving of user errors. A code ...
متن کاملHandling Rearrangements in DNA Sequence Alignment
Sequence alignment is one of the core problems of bioinformatics, with a broad range of applications such as genome assembly, gene identification, and phylogenetic analysis [1]. Alignments between DNA sequences are used to infer evolutionary or functional relationships between genes. Evolution occurs through DNA mutations, which include small-scale edits and larger-scale rearrangement events. T...
متن کاملCAP3: A DNA sequence assembly program.
We describe the third generation of the CAP sequence assembly program. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 5' and 3' low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also...
متن کاملA new DNA sequence assembly program.
We describe the Genome Assembly Program (GAP), a new program for DNA sequence assembly. The program is suitable for large and small projects, a variety of strategies and can handle data from a range of sequencing instruments. It retains the useful components of our previous work, but includes many novel ideas and methods. Many of these methods have been made possible by the program's completely...
متن کاملRealigner: a Program for Reening Dna Sequence Multi-alignments
We present a round-robin realignment algorithm that improves a potentially crude initial alignment of an assembled collection of DNA sequence fragments, as might, for example, be output by a typical fragment assembly program. The algorithm uses a weighted combination of two scoring schemes to achieve superior multi-alignments, and employs a banded dynamic programming variation to achieve a runn...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 1982
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/10.1.61