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Forum: Illumina/Solexa 01-18-2012, 11:25 AM
Replies: 3
Views: 4,282
Posted By bbsinfo
what is the best software to use to analyze illumina NGS data?

i am using Geneiou pro in our lab to assemble the data from NGS.
How about you guys?
Forum: Bioinformatics 01-06-2012, 07:55 AM
Replies: 0
Views: 944
Posted By bbsinfo
recomend a software to detect splice sites on plant genes?

Hello, I need a software for me to use to detect splice sites on genes to find introns on genes.
I find a website http://genes.mit.edu/GENSCAN.html

which is for vertebrate, and maize.

I am...
Forum: Bioinformatics 01-03-2012, 12:17 PM
Replies: 0
Views: 1,134
Posted By bbsinfo
MFold question

Hello, I am very new to field of studying RNA secondary structure. I am working with algae organelle genome. In mitochondrial genome, I have about 25 tRNA genes, and 3 rRNA genes.
I would like to...
Forum: Bioinformatics 01-03-2012, 07:33 AM
Replies: 13
Views: 3,052
Posted By bbsinfo
Hello, you guys, I think this post answered some...

Hello, you guys, I think this post answered some of my questions. I am also relatively new to NGS. I have used this technique to sequence organelle genomes of some algae. I got it from reading the...
Forum: Bioinformatics 01-03-2012, 07:26 AM
Replies: 12
Views: 2,956
Posted By bbsinfo
how do you guys find possible introns on a gene?...

how do you guys find possible introns on a gene? Which software do you use?
Forum: General 01-03-2012, 07:06 AM
Replies: 7
Views: 4,003
Posted By bbsinfo
Thank you so much for your helps. I think I...

Thank you so much for your helps. I think I finally could select more than one sequences in bioedit. I greatly appreciate your help.
So I run clustalW on my data, the score it gives me for example...
Forum: General 12-30-2011, 10:16 AM
Replies: 7
Views: 4,003
Posted By bbsinfo
Hello, first of all, thank you so much for...

Hello, first of all, thank you so much for sharing all these with you.
I have two sequence that I saved seperately as two file.
I read the help file that to select two files , press shift key.
but...
Forum: Illumina/Solexa 12-30-2011, 10:05 AM
Replies: 2
Views: 1,854
Posted By bbsinfo
i have assembled organelle genome

i have assembled organelle genome
Forum: Illumina/Solexa 12-29-2011, 06:55 AM
Replies: 2
Views: 1,854
Posted By bbsinfo
how do you find a possible intron on a gene?

hello all, i am relatively new here. I am wondering how do you guys find a possilbe intron on a gene? what are the criterias? what software do you use?
thanks
Forum: General 12-29-2011, 06:54 AM
Replies: 7
Views: 4,003
Posted By bbsinfo
anyone who have used the software BioEdit before?

Hello, everyone. I am wondering whether anyone here has used BioEdit before to compare how similar two genomes are?
Recently, I have been trying to compare two organelle genomes by using this...
Forum: Illumina/Solexa 12-02-2011, 12:54 PM
Replies: 0
Views: 1,382
Posted By bbsinfo
how can i decide the exact start and end of rRNA on mitochondria

Hello. I am using next generation sequencing to get mitochondrial genome of algae.
I know how to determine the start and end of a protein coding gene, but I am confused about the start and end of a...
Forum: General 04-20-2011, 07:10 AM
Replies: 9
Views: 3,047
Posted By bbsinfo
Long-range-PCR

Hello, Can anyone tell me whether there is any difference in designing primers for long-range PCR compared to designing primers for ordinary PCR?
Many thanks.
Forum: General 04-20-2011, 07:03 AM
Replies: 5
Views: 3,134
Posted By bbsinfo
And I also have another confusion. I realized...

And I also have another confusion. I realized that some people believe that if you mention "genomic DNA" that only means nuclear DNA. But I have read paper, in which people use "genomic DNA" to refer...
Forum: General 04-20-2011, 06:59 AM
Replies: 5
Views: 3,134
Posted By bbsinfo
You have to do extra selective lysing or...

You have to do extra selective lysing or centrifuge before you perticipate your DNA pallets, am I right? Many thanks!
Forum: General 04-19-2011, 04:50 PM
Replies: 5
Views: 3,134
Posted By bbsinfo
The DNA extracted by kit contain only nucleus DNA?

Hey, I am very new, please bare with my stupid question. Does the DNA extracted by extraction kit contain only nuclear DNA? Or it also contain organalle DNA, such as mitochondrial DNA and plasmid...
Forum: General 04-14-2011, 01:42 PM
Replies: 9
Views: 3,047
Posted By bbsinfo
Do you mind telling me what is WGS?

Do you mind telling me what is WGS?
Forum: General 04-13-2011, 11:10 AM
Replies: 9
Views: 3,047
Posted By bbsinfo
mitochondrial genome

Hello, everyone, I am new here. I need some suggestion or thoughts on this question I have.
I plan to sequence mitochondrial genome of a plant. So I need to figure out a way to design primers to...
Forum: General 04-13-2011, 07:17 AM
Replies: 54
Sticky: NGS Blogs
Views: 73,203
Posted By bbsinfo
If you are asked to pick the best blog from all...

If you are asked to pick the best blog from all these choices, what would it be?
Thanks
Forum: Introductions 04-13-2011, 06:33 AM
Replies: 373
Views: 122,142
Posted By bbsinfo
Hello, my name is Amy. I am very new here. I just...

Hello, my name is Amy. I am very new here. I just started to read something about 2nd generation sequencing. I might need it in the future. Looks like there are a lot to learn. Hope you guys dont...
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