BLASTn results of sequenced PCR fragments versus NCBI nucleotide collection (nr/nt) and NCBI candidate gene reference EST.Steve, BabbenDragan, PerovicMichael, KochFrank, Ordon
(Ref. 2) The nucleobases that make up the nucleic acid are used to distinguish DNA from RNA molecules. In DNA, thymine complementary pairs with adenine whereas in RNA, uracil matches with adenine. The pairings of nucleobases C-G and A-T (or A-U in RNA) are referred to as base ...
The BLAST software package for sequence alignment is one of the most fundamental and widely used bioinformatics tools [1] [2]. Given the large population of BLAST users, any improvement in the execution speed of BLAST will bring significant benefits to the bioinformatics community. Some research ...
G-BLASTN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. G-BLASTN can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when ...
如上所示,我事先利用makeblastdb建好了名为[1]的自建库,打算用它比对tmp.fasta。于是输入以下命令: blastn-query./tmp.fasta-db./-outfmt7-perc_identity80-evalue0.00001-num_threads8-outCas_arg_blast1.txt 结果报错:BLASTDatabaseerror:Noaliasorindex file foundfornucleotide database[./]insearch...
基因组平均遗传相似度(Average nucleotide identity,ANI)是指两细菌个基因组之间同源基因的相似性。 ANI 值可以通过两种运算方法得出:一种是以MUMmer 运算法则为基础(ANIm);另一种是以BLASTn 方法为基础(ANIb),相比之下后者应用更为广泛。普遍认为亲缘关系较近的种群间ANI值至少为70%−75%,而定义一个种的ANI ...
BlastAlign uses NCBI blastn to build a multiple nucleotide alignment and is intended for use with sequences that have large indels or are otherwise difficult to align globally. The program builds a matrix representing regions of homology along the sequences, from which it selects the 'most repr...
Gene annotation and comparative genome analyses (BLASTN, BLASTX) were performed against a custom database of 11 previously published cp genomes using default parameters of 60% for protein coding genes and 85% for tRNAs and rRNAs. For genes with low amino acid sequence identity, manual ...
Two adjacent nucleotide-binding site-leucine-rich repeat class genes are required to confer Pikm-specific rice blast resistance Ashikawa I, Hayashi N, Yamane H, Kanamori H, Wu J, Matsumoto T, Ono K, Yano M (2008) Two adjacent nucleotide-binding site-leucine-rich repeat class genes are requi...
Plant small RNAs are important regulatory elements that fine-tune gene expression and maintain genome integrity by silencing transposons. Reproductive organs of monocots produce abundant phased, small interfering RNAs (phasiRNAs). The 21-nt reproductive