Rna Seq Alignment Comparison Essays


Found 36138 essays.

Report on RNA-seq Transcriptomics

Alignment and classification of reads to reference genome or transcriptome.In order to visualise the alignment of the tb1 sample to the reference genome, we had to import import the fasta formatted reference genome and tophat2 generated alignment .bam file... .. Transcriptomics is the field of biology that studies the RNA transcripts in a large scale manner.The most effective method in analysing RNA both qualitatively and quantitatively is next generation sequencing.Argonaute CLIP-seq detects the Argonaute associated RNA to predict miRNA targets, while BRIC-seq is used to measure half-life of RNA transcripts.


2172 words (5.4 pages)
Transcript Expression Level of White Kelampayan

The corrected p-values will be set with default calculations: Bonferroni corrected p-values or FDR corrected p-values.Expression analysis of samples will be observed and recorded.The comparison of gene expression between samples can be directly determined once RPKM is used.The preparation before analysis such as sample collection, RNA isolation, cDNA library construction, sequencing and mapping are done.The functional annotation of RNA-seq data from white kelampayan will be expected to be defined in term of gene ontology via Blast2GO program.


1912 words (4.8 pages)
Understanding an Unknown Protein Sequence

This does show that the query protein is the predicted protein with Seq ID: gi|168001481|ref|XP_001753443.1 as we have found out previously.It may also be that the second protein in the similarity match, Seq ID: gi|168035394|ref|XP_001770195.1 may be distantly related to the query protein.When a report was generated for the predicted protein of Physcomitrella patens Seq ID: gi|168001481|ref|XP_001753443.1, it is clearly seen that Physcomitrella patens has 4 hits, followed by Selaginella moellendorffii that has 2 hits.The ability of researchers to utilise RNA interference methods and also gene targeting has allowed the study of gene function and the subsequent study of the protein function using the many bioinformatics tools in order to p...


2749 words (6.9 pages)
Prioritising Drug Targets for Antimalarial Drugs

According to the related research, ATP-binding contains biological processes including translocation of various substrates across membranes and non-transport-related processes such as translation of RNA and DNA repair, which need the energy of adenosine triphosphate (ATP).2004, (1):1-11. .2002, (6906):527-31. ... Zuegge J , Ralph S , Schmuker M , McFadden GI , Schneider G : Deciphering apicoplast targeting signals–feature extraction from nuclear-encoded precursors of Plasmodium falciparum apicoplast proteins.Florens L , Liu X , Wang Y , Yang S , Schwartz O , Peglar M , Carucci DJ , Yates JR 3rd , Wu Y : Proteomics approach reveals novel proteins on the surface of malaria-infected erythrocytes, Mol Biochem Pa...


1902 words (4.8 pages)
CRM Prediction and CRM Validation Approaches

Another commonly used database website is the University of California Santa Cruz (UCSC) Genome Browser Database, which provide all aspects of information for CRM prediction including experimental (DNase hypersensitivity clusters, epigenetic marks of histone proteins, and binding of transcription factors from ChIP seq) as well as computational (conservation level among vertebrates from DNA sequence alignment) study[181].Apart from structural genes, miRNAs, small non-coding RNAs which control gene expression at post-transcriptional level through hybridization with the mRNA templates and subsequently leading to translation inhibition or RNA degradation[227], are implicated in HCC progression due to the evidences on differential miRNA expre...


2745 words (6.9 pages)
Controlling Pol II Pausing

Last, global or precision nuclear run-on sequencing (GRO-seq, PRO-seq) maps transcriptionally engaged Pol II that can resume RNA synthesis (Core et al., 2012; Core et al., 2008; Kwak et al., 2013).Therefore, pausing may function as a checkpoint for RNA processing before proceeding into productive elongation (reviewed in Adelman and Lis, 2012).It is present ubiquitously in early embryos, then becomes restricted to the central nervous system (CNS), the peripheral nervous system (PNS), the brain, and imaginal disc primordia later in embryogenesis (Giannios and Tsitilou, 2013; Pearson et al., 2012; Staudt et al., 2006).Checkpoint of early elongation: Pol II carrying Ser5P serves as a platform to interact with the 5’ capping enzyme, which add...


2262 words (5.7 pages)
Analysis of GATA3 ChIP-seq in the Four Cells

In addition, the specific regulation of GATA3 in the four tumor cells need to be demonstrated in combination with experimental data.Bowtie2 allows mismatch and gap, and could make alignment very fast and memory-efficient.However, due to large amount of specific GATA3 target genes in the four tumor cells, we could not find the specific regulatory mechanism in the four tumor cells.Then GATA3 ChIP-Seq data was subjected to pairwise comparison and identification of GATA3 binding site.Then, we performed pairwise comparison of GATA3 ChIP-Seq data and identified GATA3 binding site.


2788 words (7.0 pages)
Genes and Mechanisms in Colorectal Cancer (CRC)

Their related pathway bile secretion may be potential pathogenic mechanisms of CRC.Genes such as PTGS2, CXCL3, IL8, ABCG2, ATP1A2 and AQP8 may be potential therapeutic target genes for CRC.reported that AQP8 was mainly expressed in paraneoplastic normal tissues and barely expressed in CRC cells [39].Water molecules play a key role in the modulation of the tumor microenvironment, tumorigenesis and tumor metabolism [37].However, further studies are still needed to confirm our results.


2192 words (5.5 pages)
Essay on Miss Havisham in Great Expectations

Victorian Studies 37 (1993): 73-97.11 June 2015. ."Bodies of Capital: Great Expectations and the Climacteric Economy."18 June 2015. .29 June 2015. .


407 words (1.0 pages)
Encoding RIP from Elaeis Guaneensis Jacq

The RNA was dissolved in 5ml diethypyrocarbonate (DEPC) – treated water.Precipitation of RNA was performed by adding 0.1 vol of 3M sodium acetate (pH 5.2), 2 vol 100% ethanol and incubated at -80°C for overnight.Figure : Total RNA from various treated and untreated oil palm tissues.The RNA integrity was examined using 1.5% agarose gel electrophoresis.The RNA was treated with DNase I (Qiagen, USA) following the manufacturer’s instructions.


2168 words (5.4 pages)
Strategies of Gene Sequencing

In order to identify the RNA polymerase binding sites, the sites of which regulatory proteins attach to the DNA are search primarily.Genes are transcribed at these promoter sites: TTGACA at -35 region and TATAAT at -10 region by RNA polymerase.The alignment can be improve by introducing an extra gap into one of the sequences, rather than taking an alignment of sequences as an absolute, so as to aid towards the formation of evolutionary relationships.These ‘words’ is used to select the two ideal alignment and then followed by computing a score for the optimal alignment.They compared customize sequences to yield a matrix of pairwise alignment scores.


2170 words (5.4 pages)
Novel Sequential-presentation-only (SPO) Line-up Effects

Lindsay and Wells (1985) devised the sequential line-up (SEQ) procedure as a better alternative.(1), 277-295. .In comparison, target-absent conditions risk foils with the closest resemblance to be picked, in effect producing more false alarms.A post-hoc analysis using the Bonferroni correction for multiple comparisons showed significant difference in the hit rate between the SIM condition and the SEQ condition ( = 0.08, < .001) and between the SIM and SPO condition ( = 0.05, = .02), but not between the SEQ and the SPO condition ( = 0.04, = .10).The first hypothesis was partially supported as there were fewer hit rates but not false alarms in the SEQ condition.


2683 words (6.7 pages)
Genome Comparison Techniques Essay

It is a program which performs a local alignment between two nucleic or protein sequences.In 1972, the first real sequencing of a genome is published, with the reading of the RNA sequence of the gene of the Bacteriophage MS2 virus.Data processing for bioinformatics applications is currently done by software, which often takes a long time, even aligning a few hundred sequences using multiple alignment tools consumes several CPU hours on ultramodern workstations.Multiple Single Instruction Data Flow (SIMD) paradigm is heavily used in this class of processors, making it suitable for parallel data applications such as sequence alignment.The Needleman-Wunsch Algorithm is used to obtain the global alignment of two sequences proteins or nucleic...


3343 words (8.4 pages)
Molecular Heterogeneity of Carnation Mottle Virus in Iran

.. CarMVcoat protein gene sequences used in sequence comparison and phylogenetic analysis .. .Total plant RNA was isolated from CarMV–infected leaf tissues using sodium lauroyl sarcosine (Barzegar et al., 2005) and was applied in reverse transcription (RT) reaction to synthesis first cDNA strand using RevertAidFirst Strand cDNA Synthesis Kit (Fermentas, Vilnius, Lithuania) according to the manufacturer’s instruction.The phylogenetic tree constructed from multiple sequence alignment of the CP nucleotide sequence of Iranian isolates and some other isolates available from GenBank showed that the isolates collected from central parts of Iran have close relationship to the nl-2 isolate of Spain with 98.5 % sequence identity while northern i...


2151 words (5.4 pages)
DNA worksheet Essay

From here the process of converting the RNA information into amino acids begins, eventually forming a protein.The first stage in the flow of information is DNA.The functions of an organism reply on these proteins.It stores the necessary instructions for the building of protein.DNA is can be viewed as the blueprints required to start the process.


406 words (1.0 pages)
Categories of Multimeters for Electronics

To register the supreme accuracy from the relative precision of a multimeter include the outright exactness of the gadget used to align the multimeter to the relative precision of the multimeter .Other wave shapes require another alignment factor to relate RMS and general esteem.Relative exactness is the mistake of the evaluation compared with the gadget used to align the multimeter.Figure SEQ Figure \* ARABIC 1 .Producers can give alignment benefits so new meters might be bought with authentication of alignment showing the meter has been changed by norms traceable to, for instance, the US National Institute of Standards and Technology (NIST), or other political principles association.


2884 words (7.2 pages)
Classification of viruses Essay

Genetic information is stored in the form of RNA.The genome of RNA viruses can be encoded in two different directions: either the genes are stored in the 5 '→ 3' direction (positive or + polarity), such as that in which the genes are encoded in the messenger RNA of cells, either they are stored in the opposite direction (negative or - polarity).Genetic information is encoded in the form of RNA.RNA is present in cells as an intermediary when genes are translated into proteins.However, a step towards a phylogenetic classification was taken in October 2018 with the recognition by the ICTV of the grouping of negative-polarity single-stranded RNA viruses into one branch, two sub-branches and six classes.


628 words (1.6 pages)
Endosymbiotic Theory The Modern Or Organelle Biology Essay

Table 2 : A comparison of the mitochondrial genes of the Homo sapiens and Reclinomonas americana.Many phylogenetic analyses that were based on 5S rRNA sequences showed amino acid sequences similar in the mitochondria and plastid to many purple and cyano-bacteria respectively.Mitochondria and plastids share many similar characteristics including antibiotic sensitivity, cell division by binary fission, circular DNA and 70S ribosomes... Phylogenetic analyses based on ribosomal RNA (rRNA) sequences are one of the standard methods of inferring relationships among diverse organisms.Lactose uptake is controlled by an operon in prokaryotic organisms, with the binding of RNA polymerase blocked by a repressor protein, but is not in eukaryotic or...


4033 words (10.1 pages)
Chemistry of Biomolecules Essay

Viral double-stranded RNA are cut into pieces (about 21 base-pairs), called small interfering RNA (SiRNA) by the protein Dicer.Researchers use these small RNA molecules to fight disease, for instance, using them to knock out cancer genes.Based on this principle, we can synthesize a non-natural interfering RNA, then insert it into a cell to destroy any messenger RNA that we desire.In this way, the cell removes all viral messenger RNA that is the same as the original double-stranded piece found and processed by dicer.If it finds some, it cleaves the RNA, destroying it.


1802 words (4.5 pages)
Genes of Calcium Transporters

These sequencing strategies does not need prior knowledge of gene sequences thus allowing de novo assembly of transcripts in non model species that lack a reference genome and discovery of noval genes and expression profiles under specific condition.This would not only help in understanding the mechanism of calcium accumulation in finger millet but would also open newer vistas in nutritional enrichment of crops while still retaining agronomically favorable characteristics.Since, calcium is an important macro nutrient in human diet and the accumulation of calcium in some cereal grains like finger millet is high, it is necessary to understand the molecular basis of high grain calcium in cereals grains.The present investigation was carried ...


2307 words (5.8 pages)
Sequence alignment Essay

Indeed, we more simply compares amino acids or nucleotides in pairs, but within a column of multiple alignment.To achieve multiple alignment, it is necessary to generalize the notion of a score function defined above for two sequences.Most biological sequence alignment methods, and in particular protein sequence alignment methods, seek to optimize an alignment score.Where M is the similarity matrix and Xi and Xj correspond to the amino acids (or nucleotides) found in the column, at the level of lines i and j of the alignment.Consists of calculating the similarity score, sorting the most similar sequences and then making a final alignment.


1519 words (3.8 pages)
Difference Between Prokaryotic and Eukaryotic Transcription

Once RNA synthesis is initiated, σ dissociates after RNA is 8-9 bases long and then the core enzyme brings about elongation of mRNA.Ans: The functions of Pol I is Ribosomal RNA synthesis, Pol II is mRNA synthesis and Pol III is tRNA synthesis, 5S and other small RNA synthesis.During transcription the strand which is complementary to RNA and serves as the template for RNA synthesis is known as?Ans: the transcription factor TFIIF accelerates RNA chain growth relatively uniformly, in concert with RNA polymerase II or pol II while transcription factor TFIIS helps elongation of RNA chain, by relieving the obstructions in the path of such elongation.Once RNA polymerase is detached, the RNA chain also comes off and the transcription terminates ...


3206 words (8.0 pages)
Adenosine Triphosphate and Aerobic Respiration Essay

Affected vs Effected 5.Empathy vs Sympathy .Terms of use | Privacy policy share x Up next Oxygen vs. Ozone.title=Cellular_respiration&oldid=320134686 Related Comparisons Oxygen vs Ozone Oxygen vs Ozone Mitosis vs Meiosis Mitosis vs Meiosis DNA vs RNA DNA vs RNA Photosynthesis vs Respiration .Animal Cell vs Plant Cell 3.


991 words (2.5 pages)
RNA structure Essay

These tetra-loop-receptor interactions are very common in three-dimensional structures of RNA and play an important role in maintaining global folding.This orientation of the sugar relative to the base determines in particular the polarity, parallel or antiparallel, of the RNA strands which are paired.We then have a structure locally associating three RNA strands.The RNA of interest is processed by either of these enzymes under very partial digestion conditions, where only zero or one cleavage occurs per RNA molecule.The tetraboucles of the GNRA family, which are among the most frequent motifs in RNA, can form long-distance interactions with helical or internal loop regions.


3066 words (7.7 pages)
Approaches Used in Phylogenetic Analysis

Therefore, it seems that mtSSU rDNA sequences can be used in phylogenetic analyses between classes and between genera.The nuclear ribosomal RNA gene exists in numerous copies in the nucleus.Mitochondrial SSU rDNA sequences are composed of conserved core regions, which arc alignablc across different classes, and variable domains, which evolve rapidly and are the loci of the majority of length mutations.They have been used in the systematics of wide range of fungi and seem not to be adequate in the systematics of genera in the same family or species in the same genus (Swann and Taylor, 1993; Wilmotte ., 1993).DNA sequence data which are most frequently used in phylogenetic analyses are 18S, 26S, ITSs and mitochondrial rDNAs because of the...


1545 words (3.9 pages)
Case Brief – Del Monte Fresh Produce Company v. Dole Food Company, Inc

, 330 U.S. 501, 508, 91 L. Ed.2d 1328, 1329 (S.D.1055, 67 S. Ct. 839 (1947)).Gulf Oil v. Gilbert .Misappropriation of trade secrets under the Florida Trade Secret Act, Florida Statutes § 688.001 et seq.


1397 words (3.5 pages)
Transcription Section of the Central Dogma

“Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II”.Molecular biology of RNA.RNA: Catalysis, splicing, evolution.RNA processing.In the elongation stage, the ribonucleotides will be added to the newly formed RNA strand and at the end there will be a termination signal which causes RNA polymerase-DNA interaction breakage and lead to the product which is called precurser mature mRNA (pre-mRNA).


2878 words (7.2 pages)
Comparative Genomics Research Benefits

Comparative genomics exploits both similarities and differences in the proteins, RNA, and regulatory regions of different organisms to infer how selection has acted upon these elements.The regulatory motifs of the Human Promoters were identified by comparison with other mammals.Yet another important finding is the gene and regulatory element by comparison of yeast species.For example, a comparison of the fruit fly genome with the human genome discovered that about 60 percent of genes are conserved between fly and human... Gene regulatory regions (also known as ‘cis-regulatory modules’) in vertebrates are poorly understood and annotated by comparison with protein-coding sequences.Understanding the ancestry of the functional elements comp...


2420 words (6.1 pages)
Oligopoly pricing: Old ideas and new tools

Figure SEQ Figure * ARABIC 4: the graph show decrease in demand for high fuel efficient cars when the price of petrol goes up .Figure SEQ Figure * ARABIC 1: when people expect civil unrest the demand is high but and the prices go up.Figure SEQ Figure * ARABIC 3 this graph shows increase in demand and price for high fuel efficient when the price for petrol increases due to taxation .Figure SEQ Figure * ARABIC 5 : Excess supplies of chicken in the market results to low demand and eventually falls in price.Source document .


1549 words (3.9 pages)
Economics question and answer Essay

Figure SEQ Figure * ARABIC 4: the graph show decrease in demand for high fuel efficient cars when the price of petrol goes up .Figure SEQ Figure * ARABIC 3 this graph shows increase in demand and price for high fuel efficient when the price for petrol increases due to taxation .Cambridge, Mass.Figure SEQ Figure * ARABIC 2: price of petrol increases when tax is imposed .Mason, OH: South-Western Cengage Learning .


1598 words (4.0 pages)

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