User: Paul

gravatar for Paul
Paul80
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80
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Location:
India
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4 months, 3 weeks ago
Joined:
7 years, 11 months ago
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Posts by Paul

<prev • 78 results • page 1 of 8 • next >
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Comment: C: How to do synteny analysis between two bacterial genome?
... Thankyou.. will try it, any web-based tool available? ...
written 5 months ago by Paul80
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How to do synteny analysis between two bacterial genome?
... I have a novel bacterial genome of 8Mb length (Genome1), which I want to compare it with existing well annotated gram-negative bacterial genome (Genome2). Could anyone suggest me a way to check how many genes in my novel species are matching with well-annotated bacterial genome? One option is to b ...
genome de-novo synteny written 5 months ago by Paul80 • updated 5 months ago by jrj.healey13k
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Comment: C: Genome annotation using COG
... Thankyou @ Nitin, the genome size is around 8Mb ...
written 7 months ago by Paul80
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Comment: C: Genome annotation using COG
... Thankyou so much for the detailed annotation @Nitin, I did a Quast quality analysis after the assembly, which showed me the following details, please let me know if I can go ahead with the assembly Statistics without reference # contigs 5801 N50 265554 N75 12966 L50 88 L75 ...
written 7 months ago by Paul80
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Genome annotation using COG
... I have some new organisms that were assembled and scaffolded using SPADES. Now, I have around 1000 of scaffolds for each organism genome. I want to functionally annotate the scaffolds against COG. I tried using webMGA. However, it requires a protein sequence as an input and I have nucleotide seque ...
annotation cog sequencing written 7 months ago by Paul80
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Genome Annotation of a new bacterial strain
... I have a new bacterial strain which I assembled using SPADES and scaffolded it using SPADES. Now to annotate the scaffolds, I used RAST. RAST has given me 8000 genes. I tried to annotate the genes using RAST. Out of 8000 genes, only 1497 genes got annotated using RAST. Could you please suggest me a ...
genome assembly sequencing annotation written 8 months ago by Paul80 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Genes which are not associated with Alzheimer's
... No, need not to be expressed in Alzheimer's @ATpoint ...
written 9 months ago by Paul80
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Genes which are not associated with Alzheimer's
... I require a set of genes which are not associated with Alzheimer's. I got a list of all genes from OMIM genemap2. However, I am unable to put a filter of genes which are not associated with Alzheimer's. Please suggest me a way to find out the genes which are not associated with Alzheimer's. ...
genes alzheimers omim written 9 months ago by Paul80 • updated 9 months ago by Michael Dondrup46k
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How do i set different threshold to get multiple values for ROC plot
... Below is the code I have written to build a SVM model. I am using ROCR package for plotting the ROC plot. library(e1071) library(caret) library(gplots) library(ROCR) inTraining <- createDataPartition(data$Class, p = .70, list = FALSE) training <- data[ inTraining,] ...
e1071 R svm threshold roc written 10 months ago by Paul80
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Microarray analysis using limma multiple groups
... I am using a dataset GSE1297, which contains gene expression for multiple groups ( `Control`, `Incipient`, `Moderate`,`Severe`). My contrast matrix for analyzing the dataset looks like the following contrast.matrix <- makeContrasts( CI = Control - Incipient, CM = Control - Mode ...
limma affymetrix microarray written 11 months ago by Paul80 • updated 11 months ago by RamRS23k

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Great Question 4 months ago, created a question with more than 5,000 views. For How to assemble contigs?
Popular Question 6 months ago, created a question with more than 1,000 views. For How to perform bidirectional BLAST?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Genome assembly contig ordering
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Popular Question 20 months ago, created a question with more than 1,000 views. For How to sort all the columns all together of a dataframe using R?
Popular Question 20 months ago, created a question with more than 1,000 views. For How to assemble contigs?
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Scholar 2.0 years ago, created an answer that has been accepted. For A: Retrieving SRA files using Taxonomic IDs
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