s******s
发帖数: 13035 | 1 以前记得是找个transposon里面的RE site, 再找一个frequent cutter,
切下来然后circlization，PCR测序。这个方法效率如何？有没有更加方
便的方法？怎么想这个circlization不怎么靠谱 |
b******n
发帖数: 4225 | 2 啥菌？有的菌可以直接用transposon上的引物测序
好像Salmonella和E. coli不能直接测序
【在 s******s 的大作中提到】
: 以前记得是找个transposon里面的RE site, 再找一个frequent cutter,
: 切下来然后circlization，PCR测序。这个方法效率如何？有没有更加方
: 便的方法？怎么想这个circlization不怎么靠谱
|
x**e
发帖数: 163 | 3 tail-pcr, inverse-pcr would be more efficient. |
s******s
发帖数: 13035 | 4 具体一点，有ref么？谢谢
【在 x**e 的大作中提到】
: tail-pcr, inverse-pcr would be more efficient.
|
s******s
发帖数: 13035 | 5 我说真核细胞里
【在 b******n 的大作中提到】
: 啥菌？有的菌可以直接用transposon上的引物测序
: 好像Salmonella和E. coli不能直接测序
|
x*****e
发帖数: 309 | 6 circlization挺靠谱的，我10年前在细菌里面做过。
【在 s******s 的大作中提到】
: 以前记得是找个transposon里面的RE site, 再找一个frequent cutter,
: 切下来然后circlization，PCR测序。这个方法效率如何？有没有更加方
: 便的方法？怎么想这个circlization不怎么靠谱
|
l**********1
发帖数: 5204 | 7 linker-based PCR
plus
iMapper soft:
//www.ncbi.nlm.nih.gov/pubmed/18974167
//geocachingsoftware.com/imapper.html
more details
please to to E-Book
Chapter 2:
its link:
FTP://ftp.sanger.ac.uk/pub4/theses/kong/chapter2.pdf
citation:
>Based on these expectations, a web-based server called iMapper (Insertional
Mutagenesis Mapping and Analysis Tool) was developed for the efficient
analysis of insertion site sequence reads against vertebrate and
invertebrate Ensembl genomes. Taking linker-based PCR sequence reads as
input, iMapper first scans the sequence to identify a tag sequence (TS)
derived from the end of the insertional mutagen using a local sequence
alignment (LSA) algorithm. iMapper then scans the downstream sequence for
user defined contaminating sequences, then processes the sequences to
identify the restriction site sequence used for
linker ligation during the insertion site PCR, clips out the genomic
sequence between the tag sequence and first restriction enzyme cutting site
and presents this sequence to a rapid mapping algorithm called SSAHA (102).
Insertion sites can then be navigated in Ensembl in the context of other
genomic features such as gene structures. iMapper also generates FASTA and
GFF files of the clipped sequence reads and provides a graphical overview of
the mapped insertion sites against a karyotype. iMapper is designed for
high-throughput applications and can efficiently process tens of thousands
of DNA sequence reads in a short time.
and
its References
No. 102:
//ukpmc.ac.uk/articles/PMC311141/
that Transposons E- Book
full text
FTP://ftp.sanger.ac.uk/pub4/theses/kong/abstract.pdf
FTP site //ftp.sanger.ac.uk/pub4/theses/kong/chapter1.pdf
FTP site //ftp.sanger.ac.uk/pub4/theses/kong/chapter3.pdf
FTP site //ftp.sanger.ac.uk/pub4/theses/kong/chapter4.pdf
FTP site //ftp.sanger.ac.uk/pub4/theses/kong/chapter5.pdf
FTP site //ftp.sanger.ac.uk/pub4/theses/kong/chapter6.pdf
FTP://ftp.sanger.ac.uk/pub4/theses/kong/references.pdf
FTP://ftp.sanger.ac.uk/pub4/theses/kong/appendix.pdf
original posting:
http://www.mitbbs.com/article_t/Biology/31647911.html
18th
【在 s******s 的大作中提到】
: 以前记得是找个transposon里面的RE site, 再找一个frequent cutter,
: 切下来然后circlization，PCR测序。这个方法效率如何？有没有更加方
: 便的方法？怎么想这个circlization不怎么靠谱
|
s******s
发帖数: 13035 | 8 多谢了
【在 l**********1 的大作中提到】
: linker-based PCR
: plus
: iMapper soft:
: //www.ncbi.nlm.nih.gov/pubmed/18974167
: //geocachingsoftware.com/imapper.html
: more details
: please to to E-Book
: Chapter 2:
: its link:
: FTP://ftp.sanger.ac.uk/pub4/theses/kong/chapter2.pdf
|
l**********1
发帖数: 5204 | 9 De rein.
【在 s******s 的大作中提到】
: 多谢了
|
