Comparison of DNA sequences with protein sequences
Comparison of DNA sequences with protein sequences
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DOI：
10.1006/geno.1997.4995
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发表时间：
1997-11-15
期刊：
影响因子：
4.4
通讯作者：
Miller, W
中科院分区：
文献类型：
--
作者：
Pearson, WR;Wood, T;Miller, W
序列比较程序的FASTA包已经扩展到包括FASTX和FASTY，其将DNA序列与蛋白质序列数据库进行比较，在三个框架中翻译DNA序列，并将翻译的DNA序列与蛋白质数据库中的每个序列进行比对，允许空位和移码。TFASTX和TFASTY也是新的，它们将蛋白质序列与DNA序列数据库进行比较，在六个框架中翻译DNA数据库中的每个序列，并利用空位和移码进行比对。FASTX和TFASTX仅允许密码子之间的移码，而FASTY和TFASTY允许密码子内的取代或移码。我们使用不同的缺口开放、缺口延伸、移码和核苷酸取代罚分来检查FASTX和FASTY的性能。一般来说，当查询序列包含0-10%的错误时，FASTX和FASTY的性能相当。我们还评估了FASTX和FASTY报告的统计估计。这些估计是相当准确的，除了当一个框外翻译产生一个低复杂性的蛋白质序列。我们使用FASTX扫描了生殖支原体、流感嗜血杆菌和詹氏甲烷球菌基因组中未识别或错误识别的蛋白质编码基因。我们在这三个基因组中发现了至少9个新的蛋白质编码基因和至少35个可能存在错误边界的基因。(C)北京：科学出版社.
The FASTA package of sequence comparison programs has been expanded to include FASTX and FASTY, which compare a DNA sequence to a protein sequence database, translating the DNA sequence in three frames and aligning the translated DNA sequence to each sequence in the protein database, allowing gaps and frameshifts. Also new are TFASTX and TFASTY, which compare a protein sequence to a DNA sequence database, translating each sequence in the DNA database in six frames and scoring alignments with gaps and frameshifts. FASTX and TFASTX allow only frameshifts between codons, while FASTY and TFASTY allow substitutions or frameshifts within a codon, We examined the performance of FASTX and FASTY using different gap-opening, gap-extension, frameshift, and nucleotide substitution penalties. In general, FASTX and FASTY perform equivalently when query sequences contain 0-10% errors, We also evaluated the statistical estimates reported by FASTX and FASTY. These estimates are quite accurate, except when an out-of-frame translation produces a low-complexity protein sequence. We used FASTX to scan the Mycoplasma genitalium, Haemophilus influenzae, and Methanococcus jannaschii genomes for unidentified or misidentified protein-coding genes. We found at least 9 new protein-coding genes ill the three genomes and at least 35 genes with potentially incorrect boundaries. (C) 1997 Academic Press.