User: User 7433
User 7433 • 160
- Reputation:
- 160
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- Last seen:
- 8 years, 2 months ago
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- 8 years, 10 months ago
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Posts by User 7433
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8
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... Hi there,
I have used Tajima's D and Fu and Li's statistics to assess whether my sequencing data shows evidence of deviation from neutrality. (Using DNAsp software).
The problem I have is that these tests do not give ACTUAL P values. So for Tajima's D, you get a D value and then P<0.05 for exa ...
written 8.2 years ago by
User 7433 • 160
• updated
8.2 years ago by
Casey Bergman ♦ 18k
0
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... Hi,
I am looking at LD between a SNP in one gene and three SNPS that are in the neighbouring gene and I am using Arlequin to do so..
This is what is confusing me...
SNPS 1 and 2 - derived alleles of SNP1 always occur with derived alleles of SNP2 (I can see this in the haplotypes) And..Arlequin t ...
written 8.6 years ago by
User 7433 • 160
• updated
8.2 years ago by
Lars Juhl Jensen ♦ 11k
6
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1
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7.0k
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... Hi all,
I am working with haploview to view my data and get an idea on how much LD there is across my gene.
Haploview gives three options for defining blocks of LD
1) confidence intervals -95% confidence bounds on D prime are generated and each comparison is called "strong LD", "inconclusive" or ...
written 8.7 years ago by
User 7433 • 160
• updated
8.2 years ago by
Larry_Parnell ♦ 16k
0
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1
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5.9k
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1
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... hello everyone,
Has anyone here used Arlequin to conduct a Mantel test? Or any other software to do so?
I have pairwise Fsts for 19 populations. This has been done for the exons and introns of my genes.
I want to see if there if there is a correlation between the pairwise fsts of the introns and ...
10
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1
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4.6k
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6 follow
1
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... Hi,
I am asking another ka/ks related question! I am a bit of a beginner with this stuff so go easy.
I understand the the Ka/ks ratio is used mainly for interspecies comparisons..is a way of assessing what type of selection is acting on a gene.
I know it is also usable for intraspecies comparison ...
0
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1
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5.2k
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1
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... Hi, thanks for your answer.
I have calculated nucleotide diversity (pi) and gene diversity (h) but am still interested in the Ka/Ks ratio.
So it should not make a difference if I put the intronic region between exons into the sequence or not. As technically these will be excluded anyway once I assig ...
written 8.7 years ago by
User 7433 • 160
2
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1
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5.2k
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1
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... hello everyone,
I have sequencing data for my gene from >2000 individuals. I want to look at the Ka/Ks ratio of my coding regions to assess evidence of selection.
I am aware that MEGA and DNAsp are good tools to find this out but I am confused as to what to provide the software.
I would prefe ...
written 8.7 years ago by
User 7433 • 160
• updated
8.7 years ago by
Casey Bergman ♦ 18k
0
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2
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6.1k
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... Thank you both for posting..
I am operating on windows I'm afraid!
Rob - yep my input files are literally like that..I just have 4000 odd chromosomes
I have tried inputting into Ruby exactly what you suggested, but replaced the file name with that of my own...it doesnt work - does it matter where t ...
written 8.8 years ago by
User 7433 • 160
12
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2
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6.1k
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2
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... Okay so I posted on here earlier about converting my excel file full of DNA sequences into a FASTA file for analysis with DNAsp.
I currently have columns containing 1)chromosome number 2) the DNA sequence..and I want to get
>chromosomenumber
AGTAGAGATAGAGAGA....
>chromosome number
AGTCGCTCGA ...
4
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3
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7.7k
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3
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... Hi there,
I have an excel file which contains DNA sequence information (over 7000 nucleotides) for 4000 chromosomes. I want to create a fasta file that gives the nucleotide sequence for each chromosome..like this
>chromosome1
AGTGATGCGCGCTCGCGCTCGCCTCCGGCGCGCGT...
>chromosome2
GCCGCTCGCTCGCT ...
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