Sequence data
Relationship estimation from whole-genome sequence data.
... (SNP) data can greatly improve the power and accuracy of genetic relationship ...WGS data for 1490 known pairwise relationships among 258 individuals in 30 families along with 46 population samples as ...
12
Using whole-genome sequence data to predict quantitative trait phenotypes in Drosophila melanogaster.
... [17,18]. Sequence-based predictions will therefore be relevant for prediction of risk disease and individualized medicine in humans, and for genome-based selection in farm animals and ...genome sequence ...
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Self-regulating Exploration for Orthologous in Homologous Hematologic Gene Sequence Data Using UPGMA Method
... gene sequence from homologous gene ...gene sequence data and discover the relationship between hematologic genetic disorders through phylogenetic tree reconstruction using UPGMA (Unweighted Pair ...
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Phylogeny of minute carabid beetles and their relatives based upon DNA sequence data (Coleoptera, Carabidae, Trechitae)
... Within trechites, evidence is presented that Tasmanitachoides is not a tachyine, but is instead a mem- ber of Trechini. Perileptus is a member of subtribe Trechodina. Against Erwin’s hypothesis of anillines as a ...
32
Identifying selection in the within-host evolution of influenza using viral sequence data.
... We have here described a framework for the inference of selection acting upon a viral population within an individual host, based upon time-resolved sequence data. Within-host selection is of importance for ...
13
Can abundance of protists be inferred from sequence data: a case study of foraminifera.
... on sequence abundance of SSU rRNA gene in ...the sequence abundance was ...raw sequence proportions as well as to the sequence abundance normalized by rDNA copy number and rRNA expression ...
8
ToPS: a framework to manipulate probabilistic models of sequence data.
... We presented ToPS, an open-source object-oriented framework for analyzing probabilistic models of sequence data. It implements seven well-established probabilistic models that have applications in many ...
10
Sequence to Medical Phenotypes: A Framework for Interpretation of Human Whole Genome DNA Sequence Data.
... variant data from whole genome, exome, and targeted re- ...genome sequence data in apparently unrelated individuals yields a parsimonious set of variants for manual review (~100) that may have ...
15
CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data
... samples, sequence data must be in fastq format but can either be paired-end or single-read ...fastq data so that must be done before running the program if desired (for issues surrounding quality ...
11
Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses.
... short-read sequence data and, because simulated reads may not always accurately represent errors that appear in actual datasets, we assembled reads obtained from sequencing runs of varying qualities ...
10
Concatenator: sequence data matrices handling made easy
... Sequence data files can be organized in many different formats. Different sequence analysis software require differently formatted input files. The FASTA format has become very popular due to its ...
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A unified method for detecting secondary trait associations with rare variants: application to sequence data.
... Standard permutation algorithms cannot be applied to obtain empirical p-value. This is because when the primary and secondary traits are correlated and the genetic region is associated with the primary trait, neither the ...
13
An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data.
... sequencing data allowed us to estimate the average lengths of transcripts in different tissues and we found that brain expressed mRNAs with 39UTRs 300–400 bp longer on average than in other ...
11
A horizontal alignment tool for numerical trend discovery in sequence data: application to protein hydropathy.
... 59% sequence identical to A2a (Figure ...pairwise sequence identity to A2a (Figure 5B) and its structure has not been experimentally determined [60], this observed similarity was consistent with an ...
13
Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data.
... multilocus sequence analysis (MLSA) of gyrase B the b-subunit of DNA topoisomerase (gyrB), 16S rRNA (16S), subunit A of SecA preprotein translocase (secA1), 65 kDa heat shock protein (hsp65), and RNA polymerase ...
11
Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data.
... WGS data but is not specific to the sequencing employed and should work similarly for Illumina, 454 and Pacific Bioscience read ...for data from RFLP assays or DNA microarrays with- out substantial ...
20
Towards decrypting cryptobiosis--analyzing anhydrobiosis in the tardigrade Milnesium tardigradum using transcriptome sequencing.
... Illumina sequence data was analysed using SolexaQA version ...used. Sequence reads are available at the SRA of NCBI with the accession numbers SRX426237 (active), SRX426238 (inactive tun), SRX426239 ...
15
Sequence polymorphism from EST data in sugarcane: a fine analysis of 6-phosphogluconate dehydrogenase genes
... ters. Sequence alignment was occasionally corrected man- ually, especially near the ends of alignments, because INDEL delineation may not have always been well man- aged through the sequential cycles of group ...
7
Strategies for metagenomic-guided whole-community proteomics of complex microbial environments.
... metagenomic sequence data, a FDR was estimated at the peptide level using an established method of reverse database searching [34,35] for each metagenomic processing method for a total of 6 target-decoy ...
11
Searching Most Likely DNA Sequence Using HMM
... given sequence data, ...DNA sequence directly, without making the preprocessing step of extracting all possible ...DNA sequence using hypothetical ...
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