User: jackuser1979

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jackuser1979860
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Posts by jackuser1979

<prev • 110 results • page 1 of 11 • next >
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Identifying core proteins -Pangenome
... I want to identify core proteins from pangenomic study. For this I used online tool Panseq(https://lfz.corefacility.ca/panseq/page/pan_full.html). In this tools, we have option to select full genomes of different strains,and it outputs result in coregenome fragments, and accessory genome fragments ...
coregenes coreproteins pangenome genomics written 23 months ago by jackuser1979860 • updated 23 months ago by dago2.5k
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Molecular Dynamics simulation -Necessity
... Is Molecular Dynamics simulation is always necessary for  docked homology modeled protein (protein-ligand) ?. In which cases you can defend it is not needed? ...
molecular dynamics md homology model protein written 4.4 years ago by jackuser1979860
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Differential gene expression analysis- different methods
... One of my collegue outsourced the data analysis and they followed below method in finding differential expression analysis First they did, denovo assembly of controlA, controlB, treatedA and treated B separtely. Assembled transcripts from all the samples were iteratively clustered to produce uni-tr ...
differential gene expression denovo assembly written 4.7 years ago by jackuser1979860 • updated 3.9 years ago by Biostar ♦♦ 20
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insilico method to infer regulatory mechanism of protein
... What are the ways to elucidate the regulatory mechanisms of the secreted proteins in plants through bioinformatics approach? ...
sequence written 4.8 years ago by jackuser1979860 • updated 4.7 years ago by Biostar ♦♦ 20
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Gene expression-comparing replicates
... I have normal tissue (replicate A1 and replicate A2) and abnormal tissue (replicate B1 and replicate B2). I would like to do gene expression analysis. I don't have close reference genome. I would like to denovo assemble all samples (normal tissue and abnormal tissue transcripts) and do read mapping ...
gene expression rna-seq written 4.9 years ago by jackuser1979860 • updated 4.7 years ago by Biostar ♦♦ 20
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Answer: A: What Next After Assigning Function To An Unknown Protein
... I think you just ran interpro scan and identified new domain. Try blast search with other fungal genomes & genbank nr database, examine if you can find any homologues to your protein sequence. Next you can go for homology modelling, try searching your sequence in PDB database using blast and y ...
written 5.0 years ago by jackuser1979860
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Answer: A: Fastqc, Trimming And Kmers
... Have you checked FastQC website?. These examples will give you an idea whats wrong with your sequence: Overrepresented Kmers: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/3%20Analysis%20Modules/11%20Overrepresented%20Kmers.html Sequence Length Distribution: http://www.bioinformat ...
written 5.0 years ago by jackuser1979860
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Answer: A: How To Find Novel Genes From Comparative Transcriptomics?
... I assume you don't have reference genome. So you can do comprehensive denovo assembly combining both plant sequence reads. Then map the reads of these two plant reads to the denovo assembly and can do differential gene expression analysis. Any differential gene expression finding tools like DEseq, E ...
written 5.0 years ago by jackuser1979860
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Answer: A: Best Free Text Editor For All Popular Languages (R, Python, Perl Etc..)
... I use vim on linux and gvim on windows. gvim on windows very good utility to open large file data (like NGS). ...
written 5.1 years ago by jackuser1979860
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Answer: A: Jellyfish-Kmer, Genome Size Estimation
... To answer my own question, there is available perl script to get k-mer distribution from jellyfish with nice plot developed by Joesphryan. ...
written 5.1 years ago by jackuser1979860

Latest awards to jackuser1979

Popular Question 3.6 years ago, created a question with more than 1,000 views. For Differential gene expression analysis- different methods
Great Question 3.6 years ago, created a question with more than 5,000 views. For R-Making Piechart By Groups
Good Answer 3.6 years ago, created an answer that was upvoted at least 5 times. For A: Which Is The Best Way To Do Protein Function Prediction
Epic Question 3.6 years ago, created a question with more than 10,000 views. For Jellyfish-Kmer, Genome Size Estimation
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Vcf To Gff Format
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Snp Cluster Analysis
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Functional Annotation With Ensembl Gene Ids
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Importing Varscan Vcf To Igv
Popular Question 3.6 years ago, created a question with more than 1,000 views. For R-Plot-Snps-Sliding Window Or Circular Plot
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Novel Snps-Dbsnp-Contigs
Great Question 3.6 years ago, created a question with more than 5,000 views. For Jellyfish-Kmer, Genome Size Estimation
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Orthology Search-Rbh Or Biomart
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Population Rate Calculation Programme
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Snp-Annotation And Effect Prediction
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Jellyfish-Kmer, Genome Size Estimation
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Comparing Cdna Sequence From Different Species
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Population Genetics Tools To Handle Ngs Data
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Nonsynonymous Mutation-Contig To Amino Acid Position
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Calculating Ds/Dn Ratio Through Contig Snp Annotation
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Variant Effect Predictor On Domain Level
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Contig-Kegg Mapping
Student 3.6 years ago, asked a question with at least 3 up-votes. For Functional Annotation With Ensembl Gene Ids
Student 3.6 years ago, asked a question with at least 3 up-votes. For R-Plot-Snps-Sliding Window Or Circular Plot
Student 3.6 years ago, asked a question with at least 3 up-votes. For Differential gene expression analysis- different methods
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Snp-Annotation And Effect Prediction

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