User: qwzhang0601

gravatar for qwzhang0601
qwzhang060170
Reputation:
70
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Trusted
Location:
United States
Last seen:
3 months, 3 weeks ago
Joined:
4 years, 10 months ago
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q**********@gmail.com

Posts by qwzhang0601

<prev • 73 results • page 1 of 8 • next >
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Answer: A: alignment with phylogenetic tree
... Thank you! Briefly, I want to show multiple sequencing alignment. Some sites under positive selection may evolve differently among different species. So I want to order the sequences according to the phylogenetic tree of those species. Thanks ...
written 3 months ago by qwzhang060170
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alignment with phylogenetic tree
... I have phylogenetic tree of 100 species, and I also have the multiple sequence alignment file for a gene we are interested in. I wonder whether there is some tool to generate a plot which shows both phylogenetic tree of the 100 species and sequence alignment of the gene from 100 species? Thanks ...
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Comment: C: obstain 100-way alignment of 100 species for a certain gene
... Thank you for your suggestion. I tried to get the alignment, but it seem it generate the alignment on the gene DNA sequence level (including noncoding part), right? I see many long gaps in the alignment. Is there a way to only include CDS sequence or protein sequence? Thanks ...
written 3 months ago by qwzhang060170
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Comment: C: obstain 100-way alignment of 100 species for a certain gene
... Thanks. I got the files (like refGene.exonAA.fa.gz) from the link you provided. But it seems, it only includes alignment on exon level. We need to merge all exons by myself. Am I right? Not sure whether there is a direct way to do this, or any tool can help to merge alignment of exons into alignmen ...
written 3 months ago by qwzhang060170
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obstain 100-way alignment of 100 species for a certain gene
... I want to get the alignment file (Amino acid for protein, and nucleotide for CDS) for a particular gene from 100-way alignment of 100 species (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/multiz100way). Is there an easy way to get it? Thanks ...
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Comment: C: Validate PCR DNA primers against whole de novel genome
... Ok. Thank you very much. ...
written 9 months ago by qwzhang060170
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Comment: C: Validate PCR DNA primers against whole de novel genome
... Many thanks. Is there a publication and manual for dicey? I am looking at MFEprimer-3.0 (https://www.mfeprimer.com/), have you tried this before? Thank you ...
written 9 months ago by qwzhang060170
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Validate PCR DNA primers against whole de novel genome
... I want to test gene copy number of some genes. I designed the primer using primer3 and what to test whether the primers are specific to my genes. I know some tools can do this. For example, I tried primer-blast, but it can not work when I test it against the whole genome (about 3G base pairs). I als ...
primers in sillico written 9 months ago by qwzhang060170 • updated 9 months ago by trausch1.4k
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Design paralog-specific primer for RT-PCR on de novel genome
... We assembled the genome of a new rodent species. We also did gene annotation. There is one gene showing expansion in our rodent genome (7 copies in our genome, 2 copies in mouse and 1 copy in human). Below show our evidence that we consider the gene are very likely under expansion. Now we want to ...
qrt-pcr primer written 10 months ago by qwzhang060170
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Comment: C: compare and merge VCF files
... It seems a little bit complex. But thanks. ...
written 13 months ago by qwzhang060170

Latest awards to qwzhang0601

Popular Question 8 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 8 months ago, created a question with more than 1,000 views. For Number of shared biological GO terms
Popular Question 8 months ago, created a question with more than 1,000 views. For nucleotide divergency (--site-pi) in VCF tools
Popular Question 9 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 12 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 12 months ago, created a question with more than 1,000 views. For Number of shared biological GO terms
Popular Question 12 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9
Popular Question 17 months ago, created a question with more than 1,000 views. For Normalized non-synonymous variant count
Popular Question 17 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9
Popular Question 17 months ago, created a question with more than 1,000 views. For Browser of 1000 genome phase 3 showing allele frequency in each population
Popular Question 17 months ago, created a question with more than 1,000 views. For nucleotide divergency (--site-pi) in VCF tools
Popular Question 20 months ago, created a question with more than 1,000 views. For Length of transcripts of mm9
Popular Question 20 months ago, created a question with more than 1,000 views. For nucleotide divergency (--site-pi) in VCF tools
Popular Question 20 months ago, created a question with more than 1,000 views. For Prepare gene families for CAFE
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Length of transcripts of mm9

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