BLASTN search with the 62 bp repeat sequence
FPGA Implementation of Wu- Manber Algorithm for BLASTN DNA Sequence Matching
... Hash collisions and duplicate keys are two common problems for simple hashing strategies. The former will hash two different queries to the same location, while the latter may miss additional position information. Both ...
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Optimization of sequence alignment for simple sequence repeat regions
... SSR repeat with the tandems GAA, GAT, and GAGGAT respec- ...the sequence tested in case ...whole sequence in case E, the phylogenic trees showed that the genetic distance of the most 24 related ...
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Sequence to Sequence Learning as Beam Search Optimization
... on sequence generation at training ...beam search optimization shows significant improvements on all three tasks, and particular improvements on tasks that require difficult ...
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Mitochondrial DNA Sequence Variation in the Eastern House Mouse, Mus musculus: Comparison With Other House Mice and Report of a 75-bp Tandem Repeat
... Mitochondrial DNA sequences: Figure 2 shows the complete sequences of the control region and flanking tRNA genes determined for one type of mtDNA from each of three comm[r] ...
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Sequence Analysis of the Direct Repeat Region inMycobacterium bovis
... the sequence of the 36-bp DR element is highly conserved between strains and species suggests that deletions have probably arisen by recombination between DR se- ...
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A Simple Sequence Repeat-Based Linkage Map of Barley
... simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence ...
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Simple sequence repeat variation in the Daphnia pulex genome
... to repeat number, motif size, motif sequence, and distribution of SSR ...with repeat number as well as motif size. For non-repeat unit polymorphisms, we identify a motif-dependent ...
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Development of expressed sequence tag and expressed sequence tag-simple sequence repeat marker resources for Musa acuminata
... flavonoid pathway genes, phytohormone biosynthesis genes, pathogenesis-related protein coding unigenes and genes involved in plant detoxification. Host receptor genes and signal transduction Distinct plant R-gene ...
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HIGH SPEED RECONFIGURABLE ACCELERATOR FOR WORD MATCHING STAGE OF BLASTN
... Alignment Search Tool) is one of the most popular sequence analysis tools used by molecular ...database search, is continuously ...genomic sequence database by using hash function to ...
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Identification of simple sequence repeat markers for sweetpotato weevil resistance
... Received: 25 January 2017 / Accepted: 19 May 2017 / Published online: 10 June 2017 Ó The Author(s) 2017. This article is an open access publication Abstract The development of sweetpotato [Ipo- moea batatas (L.) Lam] ...
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Effect of the Major Repeat Sequence on Chromosome Loss in Candida albicans
... major repeat sequence (MRS) is found at least once on all but one chromosome in Candida albicans, but as yet it has no known relation to the ...unique repeat structure and, more specifically, the ...
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RETRIEVING SEQUENCE INFORMATION. Nucleotide sequence databases. Database search. Sequence alignment and comparison
... with sequence databases NCBI (The National Center for Biotechnology Information) accepts all submitted sequences and does not check whether the sequence is accurate or ...
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A 1232 bp upstream sequence of glutamine synthetase 1b from Eichhornia crassipes is a root-preferential promoter sequence
... upstream sequence (1232 bp) was obtained and named as ...This sequence was submitted to NCBI database and assigned the accession number ...Homology search using Blast programs revealed no ...
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Replication of the retroviral terminal repeat sequence during in vivo reverse transcription.
... (B) Reverse transcriptase transfers prior to copying a mutation in the 5' r; therefore the 3' r is copied in that region and will yield a provirus with the R region of the LTRs derived f[r] ...
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Inter-Simple Sequence Repeat (ISSR) Markers: Are We Doing It Right?
... <100 bp are usually less sharp and could be the products of primer-dimer amplification; band sizes >2000 bp are difficult to amplify during PCR, and so have weak intensities and tend to have low ...
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A Tabu Search Approach to Multiple Sequence Alignment
... BLAST [3] and variations of this algorithm are some of the most commonly used heuristic local alignment programs. These programs compare DNA/ protein sequences to DNA/protein databases in order to find patches of ...
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Div BLAST : diversification of sequence search results
... and search tools need to perform diversifications tailored for each ...in sequence search and ...of sequence similarity search ...the sequence matches as bit ...
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FASH: A web application for nucleotides sequence search
... Text sequence (see Figure ...step. Sequence alignment methods are applied on all diagonals with sum above the specified ...the search, as well as the threshold, without reinvesting time in ...
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Finding and extending ancient simple sequence repeat-derived regions in the human genome
... By identifying over three million previously overlooked short and imperfect SSR loci, we provide evidence that the SSR life cycle is highly flexible and show that mul- tiple paths to SSR death exist. While some of the ...
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The Collagen Repeat Sequence Is a Determinant of the Degree of Herpesvirus Saimiri STP Transforming Activity
... on sequence divergence at the left end of genomic DNA in which the saimiri transforming protein (STP) ...cells. Sequence com- parison reveals that STP-B lacks the signal-transducing modules found in STP ...
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