User: bingyu19821270

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Posts by bingyu19821270

<prev • 10 results • page 1 of 1 • next >
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Comment: C: How To Calculate The Number Of Potential Synonymous And Nonsynonynous Sites
... Hi aidan-budd, Thank you very much for taking the trouble to help me. I really appreciate it. You are right. I'm looking for a software to count the number of potential synonymous or nonsynonymous sites of a sequence, by identifying 4-fold degenerate, 2-fold degenerate sites (Nei-Gojobori Method). ...
written 6.8 years ago by bingyu1982127040
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How To Calculate The Number Of Potential Synonymous And Nonsynonynous Sites
... Hi everyone, Does anyone know how to calculate the number of synonymous sites for a certain sequence? I know the principles, but I don't know whether there is any software or script that can be used for this. All the software I know is to calculate dN, dS, Ka, and Ks... I would really appreciate if ...
written 6.8 years ago by bingyu1982127040 • updated 2.8 years ago by a1ultima720
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Can One Use The Ensembl Api To Retrieve Multiple Alignment Between The 46 Vertebrate Species
... Hi everyone, Does anyone know whether I can use ensembl API to retrieve multiple alignment between the 46 veterbrate species as in UCSC? If it is not possible,and I have toI retrieve the alignment using UCSC, can I also retrieve the corresponding genomic coordinates in all the species? I mean, id ...
ensembl alignment coordinates written 7.3 years ago by bingyu1982127040 • updated 2.5 years ago by Biostar ♦♦ 20
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Comment: C: Fetch Codon Or Amino Acid Alignment Of Certain Genomic Intervals Among 46 Specie
... Anyhow, Thank you for being willing to help. ^_^ ...
written 7.3 years ago by bingyu1982127040
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Comment: C: Fetch Codon Or Amino Acid Alignment Of Certain Genomic Intervals Among 46 Specie
... Hi, Whetting Thank you for your answer. I also thought this might be work, but when I tried, I found that since the alignment contains many gaps in different species and at different positions, no matter which frame I chose, I could always found stop codons in several species. ...
written 7.3 years ago by bingyu1982127040
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Comment: C: From Gene Names To Sequences/Orthollogs
... Thank you, JC. I tried to homogenize my gene IDs use the tool you suggested, but there are hundreds of genes that have no hits in the database. Does this mean that the database hasn't been updated for a long time or....there is some other reason? ...
written 7.4 years ago by bingyu1982127040
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From Gene Names To Sequences/Orthollogs
... Hi all, I have a bunch of gene names (the names are in chaos, some from Refseq, some from CCDS...) in human genome. I can I get the sequences and chromosomal coordinates of these genes? If I finally get them, could some tell me how to fetch the orthologs from other veterbrate species (46 species as ...
gene sequence written 7.4 years ago by bingyu1982127040 • updated 7.4 years ago by JC9.1k
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(Closed) Get Codons Including A Certain Site On The Genome
... Hi all, I have been stuck here for quite a long time. I would be really grateful if someone can help me out. I have a list of thousands of SNP sites in human (BED format), which are all located in CDS region. I want to know what is the corresponding sites in other species, the whole codons contain ...
genome codon written 7.4 years ago by bingyu1982127040
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Comment: C: Fetch Codon Or Amino Acid Alignment Of Certain Genomic Intervals Among 46 Specie
... Thank you for replying to my question, Vikas. Not exactly. I think I didn't explain it clearly. Say, I have a specific chromosome position in human genome, like, chr3:131102053. It's in CDS region, which is an "A". First, I wanna know whether in other 45 vertebrate species it's also A or other nuc ...
written 7.4 years ago by bingyu1982127040
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Fetch Codon Or Amino Acid Alignment Of Certain Genomic Intervals Among 46 Species
... Hello everyone, In UCSC database, there are genome alignment among 46 verterbrate species. I have hundreds of genomic intervals in human. They are all located in CDS regions. I already fetched the alignment among the 46 species for each genomic interval. The thing is that I also want to know the co ...
codon alignment written 7.4 years ago by bingyu1982127040 • updated 2.1 years ago by Biostar ♦♦ 20

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