Sequence alignments
Distinguishing regional from within-codon rate heterogeneity in DNA sequence alignments
... DNA sequence alignments. This is partly a con- sequence of the fact that our software has not been optimised for computational efficiency yet, resulting in long MCMC simulation ...
12
Analysis of Chimpanzee History Based on Genome Sequence Alignments
... multiple sequence alignments from western chimpanzees, central chimpanzees, eastern chimpanzees, and ...These alignments provide orders of magnitude more genetic data for studying the history of ...
15
Noisy: Identification of problematic columns in multiple sequence alignments
... sequence alignments [5]. Since homoplasy is defined rel- ative to the unknown true tree, it is not obvious, however, how to reliably identify the homoplastic characters with- out prior knowledge of that ...
10
Improved Bayesian methods for detecting recombination and rate heterogeneity in DNA sequence alignments
... DNA sequence alignments with the HKY nucleotide substitution model (Hasegawa et ...DNA sequence alignments generated in our study, using the authors’ ...
220
Core column prediction for protein multiple sequence alignments
... Results: We develop for the first time a predictor of column coreness for protein multiple sequence alignments. This allows us to predict which columns of a computed alignment are core, and hence better ...
16
SeqTools: visual tools for manual analysis of sequence alignments
... missing/misaligned sequence and to identify splice sites and polyA sites and ...identify sequence that is not represented (or is misrepresented) and to quickly compare annotated gene models with ...
10
CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments
... structure-based sequence align- ment derived from a set of pairwise structure-based sequence alignments, and no open-source code was found that generated an alignment allowing for gaps to be inserted ...
8
Multiple Sequence Alignments in Linguistics
... multiple sequence alignments, ALPHAMALIG (Alonso et ...obtained alignments with the cor- responding column in a set of gold stan- dard ...the alignments produced by ALPHAMALIG correspond well ...
8
SVM-based Automatic Annotation of Multiple Sequence Alignments
... Abstract—Multiple Sequence alignments are a critical step in phylogeny inference. There is a lack of an appropriate approach which is capable of 1) finding the best global alignment and 2) automating and ...
8
Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions
... The sequence alignment shows the two input align- ments concatenated by the linker symbol "&", the joint secondary structure predicted by our algorithm (with δ = ...
13
RNAstrand: reading direction of structured RNAs in multiple sequence alignments
... Table 1 lists the classification rates for different threshold values c, i.e., classifying the RNA as "plus strand" for D > c and as "minus strand" for D < -c, while -c ≤ D ≤ c is inter- preted as ...
10
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
... genome sequence prior to publication; the DOE Joint Genome Institute for providing a draft Xenopus sequence prior to publication; ...comparative sequence data available at NCBI; ...
15
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 ...
114
Molecular Analysis of the Alpha Tubulin Gene from the Microsporidium, Endoreticulatus sp Zhenjiang, Isolated from Bombyx mori
... gene sequence was obtained using the RACE protocol, and deposited in GenBank ...The sequence is 1382 bp long with a 20-bp 5’-UTR, and a 42-bp ...signal sequence (AATAAA, Figure ...multiple ...
10
First report of SLC39A4 mutation in acrodermatitis enteropathica family from the Middle East
... materials). Sequence alignments using the generated sequence data of SLC39A in the 11 family members were performed (Figure 2Sup; on-line supplemental ...reference sequence (accession number ...
6
14. D. Sivalingam, R. Rajendran and K. Anbarasan
... Pairwise sequence alignments were made with BLAST and multiple sequence alignments were also made with ...the sequence alignments, dendrograms were constructed using the ...
9
A +1 ribosomal frameshifting motif prevalent among plant amalgaviruses
... Multiple sequence alignments for ORF2p from proposed and original plant amalgaviruses were also examined in detail for conserved residues including known RdRp motifs (Poch et ...strong sequence ...
9
Protein sequence and structure alignments within one framework
... of sequence align- ment using a score matrix based on similarities of class probability vectors ...pairs, alignments were calculated, models constructed and the alignment quality measured as described under ...
12
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE
... complex alignments it is often hard to find the exact posi- tions that require manual ...and sequence logos [11] are the most common meth- ods to visualize sequence ...
7
Studies on DNA barcoding of sacred plant - Ficus religiosa L.
... Pairwise sequence alignments were made with BLAST and multiple sequence alignments are made with ClustalW, and based on the sequence alignments, dentrograms were constructed ...
11