User: inayat45shaikh
inayat45shaikh • 40
- Reputation:
- 40
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- New User
- Location:
- India
- Last seen:
- 11 months, 2 weeks ago
- Joined:
- 5 years, 10 months ago
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- i*************@gmail.com
Posts by inayat45shaikh
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... I am trying to run micropred for feature assessment from microRNA sequences, but getting following error
[inayat@gibhpc1 progs]$ perl microPred.pl seq.fasta
-microPred started...
-calculating features-------------
-folding original sequences...
-calculating miPred sequential ...
written 21 months ago by
inayat45shaikh • 40
• updated
21 months ago by
genomax ♦ 80k
1
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... Hello group,
I want to predict amino acid sequence of gene after deleting a single nucleotide?
...
written 3.1 years ago by
inayat45shaikh • 40
• updated
3.1 years ago by
willgilks • 300
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...
Thanks Sean, for the response..... can you suggests some software's
I have a question, are these softwares takes input raw files or aligned bam files, i dont know about the idea of calling variants from tumor and normal raw files, but i do know little bit about calling variants from aligned bam fil ...
written 3.8 years ago by
inayat45shaikh • 40
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... Hello everyone
I am analyzing some cancer samples wherein I have mutations have been detected from normal blood sample and tumor tissue sample of the same patient. Now I am getting mutation that are present in normal but not in tumor sample. What kind of mutation is this?? As far as i know germline ...
written 4.2 years ago by
inayat45shaikh • 40
• updated
4.0 years ago by
michael.d.mclellan • 150
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... Hello,
We have data of tumor (Tissue) and Normal (Blood) control from the same patients. We want to call somatic and germline variants in the same individual.
To achieve this, We aligned Tumor and normal sample each separately with hg19 and called variants. For identification of somatic mutations, ...
written 4.2 years ago by
inayat45shaikh • 40
• updated
3.7 years ago by
graeme.grimes • 10
2
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... Hello group,
I had identified SNPs by mapping reads to scaffolds (closely related organism) and generated VCF file. The problem I am facing is in annotation. I wanted to classify these variants into exonic, intronic, synonymous, non-synonymous etc. I came across some SNP annotation pipelines I.e. v ...
written 4.4 years ago by
inayat45shaikh • 40
• updated
4.4 years ago by
Sean Davis ♦ 26k
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... Thanks for the above paper.
Paper is stating, e-values and bit scores (bits > 50) is more sensitive and reliable source for inferring homology. I had filtered blast hits based on the above parameters, but the confusion still remain, what percent of coverage (% of length of the gene sequence cove ...
written 4.4 years ago by
inayat45shaikh • 40
4
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1
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7.2k
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... Hello group,
I had predicted peptide sequences from denovo assembled contigs using abinitio (GENSCAN) approach and subjected it to similarity (BLASTP) search to identify genes in the assemble sequences. But the difficulty i am facing is with minimum percent of identity and coverage of blast hits. W ...
written 4.4 years ago by
inayat45shaikh • 40
• updated
4.4 years ago by
Renesh • 1.8k
0
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2
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2.9k
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Answer:
A: Genome Annotation Strategies
... Hello group,
I have predicted set of genes for large eukaryotic genome from ab initio (GlimmerHMM) and evidence Exonerate & BLASTX based approaches, now i want to make consensus gene sets from both the predictions. initially i was facing issue with gff files loading into mysql database due to p ...
written 5.6 years ago by
inayat45shaikh • 40
0
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1.6k
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... Hello group,
i have predicted set of genes for large eukaryotic genome from ab initio (GlimmerHMM) and evidence (Exonerate) based approaches, now i want to make consensus gene sets from both the predictions. i am facing issues with GLEAN installation, as its installation manual doesn't provide deta ...
written 5.6 years ago by
inayat45shaikh • 40
• updated
5.6 years ago by
Biostar ♦♦ 20
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For What should be the minimum percent of identity and coverage of blast hits for considering as gene sequence
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