The programs GMAP and GSNAP, for aligning RNA-Seq and DNA-Seq datasets to genomes, have evolved along with advances in biological methodology to handle longer reads, larger volumes of data, and new types of biological...
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The programs GMAP and GSNAP, for aligning RNA-Seq and DNA-Seq datasets to genomes, have evolved along with advances in biological methodology to handle longer reads, larger volumes of data, and new types of biological assays. The genomic representation has been improved to include linear genomes that can compare sequences using single-instruction multiple-data (SIMD) instructions, compressed genomic hash tables with fast access using SIMD instructions, handling of large genomes with more than four billion bp, and enhanced suffix arrays (ESAs) with novel data structures for fast access. Improvements to the algorithms have included a greedy match-and-extend algorithm using suffix arrays, segment chaining using genomic hash tables, diagonalization using segmental hash tables, and nucleotide-level dynamic programming procedures that use SIMD instructions and eliminate the need for F-loop calculations. Enhancements to the functionality of the programs include standardization of indel positions, handling of ambiguous splicing, clipping and merging of overlapping paired-end reads, and alignments to circular chromosomes and alternate scaffolds. The programs have been adapted for use in pipelines by integrating their usage into R/Bioconductor packages such as gmapR and HTSeqGenie, and these pipelines have facilitated the discovery of numerous biological phenomena. less
Parkinson's disease is characterized by the irreversible and selective loss of nigrostriatal dopaminergic *** cell line-derived neurotrophic factor(GDNF) is an essential survival and maintenance factor for adult d...
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Parkinson's disease is characterized by the irreversible and selective loss of nigrostriatal dopaminergic *** cell line-derived neurotrophic factor(GDNF) is an essential survival and maintenance factor for adult dopaminergic neurons,and is considered a promising neuroprotective candidate for Parkinson's ***,the signaling mechanisms underlying this protective effect remain unclear. MicroRNAs(miRNAs) are endogenous,non-protein-coding regulatory RNA molecules that regulate the expression and translation of target *** are involved in a number of neurodegenerative *** miRNAs and GDNF affect dopaminergic neuronal processes,but the molecular crosstalk between these molecules is not fully *** understand the molecular basis of the responses of injured dopaminergic neurons to GDNF,it is important to determine if miRNAs expression or function is modified by GDNF. The present study evaluated whether GDNF modulates miRNAs *** used microarray analysis and real-time polymerase chain reaction(RT-PCR) to determine miRNAs expression in 6-hydroxydopamine(6-OHDA)-injured MN9D cells treated with GDNF for 30 minutes,1 hour,or 3 *** found that at 30 minutes,1 hour,and 3 hours of GDNF treatment,27,46,and 70 miRNAs,respectively, were differentially expressed and,among them,26%(7 of 27),67%(31 of 46),and 100%(70 of 70) were up-regulated,while the remaining were *** GDNF treatment time increased,so did the number of differentially expressed miRNAs;the number of up-regulated miRNAs increased,and the number of down-regulated miRNAs ***,we noted that miRNA expression profiles changed quickly after a relatively short GDNF treatment,and few miRNAs showed the same direction of change at ail three time *** reflects the complexity of miRNA regulatory *** Cluster 3.0,we found that miRNAs with similar expression profiles clustered together in four *** analysis of deregula
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