a*******u
发帖数: 19 | 1 做mapping的时候，根据什么原则分段比较好？
按照蛋白的domain或者motif进行分段的话，domain两侧保留多少amino acids？
每一小的分段大小多少为好？200-300？一般分多少段？
分段的时候两个分段可不可以有交叉？
如果采取没有交叉的的分段，交叉的位置的相互作用怎么排除？
一般在domain区相互作用的可能性比非domain区高吗？ |
X******n
发帖数: 914 | 2 这个都敢来问？你不怕Ｔｉａｎｚｉ说你又在试错了？ |
l**********1
发帖数: 5204 | 3 按照蛋白的domain进行分段
domain两侧保留seven amino acid residues that is enough
please refer
Simulations with our method indicate that
a read length of 20–25 bases is optimal for gene-level expression
estimation from mouse and maize RNA-Seq data when sequencing
throughput is fixed.
//www.ncbi.nlm.nih.gov/pubmed/20022975
more answers please go to
below BACHELOR THESIS (2011)
Evaluation of data from high-throughput sequencing
//is.muni.cz/th/323639/prif_b/thesis.pdf
and its references.
【在 a*******u 的大作中提到】
: 做mapping的时候，根据什么原则分段比较好？
: 按照蛋白的domain或者motif进行分段的话，domain两侧保留多少amino acids？
: 每一小的分段大小多少为好？200-300？一般分多少段？
: 分段的时候两个分段可不可以有交叉？
: 如果采取没有交叉的的分段，交叉的位置的相互作用怎么排除？
: 一般在domain区相互作用的可能性比非domain区高吗？
|
a*******u
发帖数: 19 | 4 不明白蛋白分段mapping和sequencing有什么直接的关系
seven amino acid residues有相关的参考文献或理论依据，还纯粹是经验所得？
多谢
【在 l**********1 的大作中提到】
: 按照蛋白的domain进行分段
: domain两侧保留seven amino acid residues that is enough
: please refer
: Simulations with our method indicate that
: a read length of 20–25 bases is optimal for gene-level expression
: estimation from mouse and maize RNA-Seq data when sequencing
: throughput is fixed.
: //www.ncbi.nlm.nih.gov/pubmed/20022975
: more answers please go to
: below BACHELOR THESIS (2011)
|
l**********1
发帖数: 5204 | 5 rna-seq
知道是啥吗
不清楚的话 维基一下吧
//en.wikipedia.org/wiki/RNA-Seq
RNA-seq, also called "Whole Transcriptome Shotgun Sequencing" [1] ("WTSS")
and dubbed "a revolutionary tool for transcriptomics",[2] refers to the use
of high-throughput sequencing technologies to sequence cDNA in order to get
information about a sample's RNA content, a technique that is quickly
becoming invaluable in the study of diseases like cancer.[3] Thanks to the
deep coverage and base level resolution provided by next-generation
sequencing instruments, RNA-seq provides researchers with efficient ways to
measure transcriptome data experimentally, allowing them to get information
such as how different alleles of a gene are expressed, detect post-
transcriptional mutations or identify gene fusions.[3]
here cDNA after its transcription→ amino acids residues of protein.
至于蛋白质的In Silico mapping 2062 AC 以后找到理论了 再assemble吧 啊
就是 In Vitro 还在不断否定前人的见解呢
please go to
//www.ncbi.nlm.nih.gov/pubmed/21530591
>Surprisingly, there was no detectable homology between
PfMyb2 and Cef1 in the PFC0365w/PRP19 binding domains, even
though the yeast orthologs of PfMyb2 and PFC0365w also interact.
In fact, the only significant homology between Cef1 and PfMyb2
was in the first 233 amino acids that encode the Myb DNA-binding
domain motifs (49% identical, 70% similar). This result was unexpected
because protein interaction interfaces are generally thought
to evolve more slowly, since changing residues in one protein
would require compensating changes in the binding partner. The
interaction between PfMyb2 and PFC0365w demonstrates that this
is not always the case. A similar observation has been made for
three pairs of interacting proteins from Caenorhabditis elegans [15].
Despite the lack of homology between PfMyb2 and Cef1 C-terminal
to the MYB DNA-binding domain, the fact that PfMyb2 binds to
the P. falciparum PRP19 homolog suggests that PfMyb2 is the functional
homolog of Cef1. Since Cef1 is primarily involved in RNA
splicing, we propose that PfMyb2 functions in a similar manner
and is unlikely to act as a transcription factor.
----
ps: if you are satisfied with both replied. BAOZI one please transfer to my
mitbbs financial account.
WEI-BI 10.
【在 a*******u 的大作中提到】
: 不明白蛋白分段mapping和sequencing有什么直接的关系
: seven amino acid residues有相关的参考文献或理论依据，还纯粹是经验所得？
: 多谢
|
l**********1
发帖数: 5204 | 6 if limited to Methyl transferase, Acetyl transferase,
Protein tyrosine phosphatase to perform a structural prediction of the putative ligands.
The modelling of the domains takes into account the different ligand
orientation when necessary as well as the orientation of the important
residues involved in binding.
Please go to
//adan-embl.ibmc.umh.es/
from
//www.embl.de/
and more pls go to
//mamba.bio.uci.edu/rt95.06.16/rt_1.html
from
//www.mcb.harvard.edu/hastings/dino.html
【在 a*******u 的大作中提到】
: 做mapping的时候，根据什么原则分段比较好？
: 按照蛋白的domain或者motif进行分段的话，domain两侧保留多少amino acids？
: 每一小的分段大小多少为好？200-300？一般分多少段？
: 分段的时候两个分段可不可以有交叉？
: 如果采取没有交叉的的分段，交叉的位置的相互作用怎么排除？
: 一般在domain区相互作用的可能性比非domain区高吗？
|
