s**e
发帖数: 1523 | 1 老板让我找一个比较universal的secretory signal sequence用来表达一个蛋白（其实是
truncated的，它的细胞外的部分），然后看它在ECM里面增高之后对细胞的影响。我找
了半天都是细
菌、酵母、insect cell之类的表达比较多，直接用人类细胞表达的很少，有具体
signal
sequence的就根本没找到了。我是刚换了工作，所以对这个领域不是很熟悉，查了
pubmed上的文献，
都是蛋白自带的signal sequence，没有人工进行表达的。请大家给我指点指点，或者
给推荐个文章
看看吧！谢谢了！ |
|
q**********0
发帖数: 335 | 2 Which next-generation DNA sequencing methods is the best for measuring
nuclotide frequency in sequencing, Roche/454 FLX pyrosequencer, Illumina
genome analyzer,Applied Biosystem SOLid sequencer? Thanks. |
|
|
g**********t
发帖数: 475 | 4 你的第二个问题可以用HMMER来做，行业标准。不过只有你的"pattern"是不够的，因为
你的"pattern"并没有精确给出"weights"。如果你的"pattern"是从一堆reference
sequences里面总结出来的，你可以直接把reference sequences的alignment喂给HMMER
，HMMER会生成一个customized hidden Markov model用来寻找匹配的序列。
http://hmmer.janelia.org/ |
|
n***w
发帖数: 2405 | 5 Well, I am not an expert on this.
I think it depends on your goal.
Let's say, if I wanna express some protein, then I have to make sure that my
sequence is 100% right to avoid any mutation.
But if you just want to make sure you have a right thing after several round
of PCR, you can just roughly sequence the PCR product.
I hope more people can give input into this post.
should
sequencing |
|
w******e
发帖数: 1187 | 6 suppose I have a pool of oligos (say 100 unique sequences), each
15-20base long, biotinylated on 5' end. what's the best way
to sequence them?
I guess if w/o biotin, I can probably make ds using random primer, and then
clone into sequence vector. can I do sth similar with biotinylated oligos?
thx!! |
|
w******e
发帖数: 1187 | 7 didn't know that's an option... do you know how much would it cost? is it
possible to delineate all the hundreds of different sequences together?
all of them are made of ATCG, so I would guess different sequence could
have the same mass but different sequence?
thx! |
|
y******8
发帖数: 1764 | 8 At least, ION should be able to cut the size in half, and make 4x wells in
the same area of current chip.
Optical based sequencing is able to generate reliable basecall with 20 DNA
molecules in a clone. With this number, pH based signal will be very noisy.
If ION put the price tag as 150k for future sequencer, it would be hard to
say which strategy will win in the end. |
|
k*******s
发帖数: 214 | 9 The fast way is to PCR the target region and sequence. If only one mutation
, there will be two peaks at the specific sit and it can seen from the
sequencing chromatograph.
answers
.
I
sequence |
|
y*****w
发帖数: 146 | 10 实验课题需要用到Yeast GAL1和GAL10 promoters.在addgene 上查到了GAL1 promoter
sequence， 但是怎么google都查不到GAL10 promoter sequence。有谁知道Yeast
GAL10 promoter sequence? 请发邮件至y******[email protected] 十分谢谢! |
|
u*********1
发帖数: 2518 | 11 我觉得你要解释更清楚点这到底是什么数据
一般的sequencing reads的数据，首先最短的reads也有36bp，其次所有的base都是有
想对应的phred value的；所以你这肯定不是sequencing数据
印象中一般都是reference genome是fasta格式，所以我猜测你这是什么species的ref
sequence？但不懂后面的1，2是什么意思。
总之不知道是什么。还求高人指点。 |
|
l**********1
发帖数: 5204 | 12 plus 各取所需 用C++ or Perl or python or R etc 取决于生信分析的对象
样品数量和目的项目
比如楼主的问题 如是 NGS high.through raw data 也可 try python based
Bcbio-nextgen
cited,
Summary: Python scripts and modules for automated next gen sequencing
analysis. These provide a fully automated pipeline for taking sequencing
results from an Illumina sequencer, converting them to standard Fastq format
, aligning to a reference genome, doing SNP calling, and producing a summary
PDF of results
web link:
HTTP: //seqanswers.com/wik... 阅读全帖 |
|
u*********1
发帖数: 2518 | 13 需要测某个exon，那么自然在exon的两侧设计primer；而且我故意把primer设计的距离
exon比较远（比如60-70bp），就是希望整个coding区域都可以被sequencing覆盖到。
但毕竟primer不是想在哪里设计就在哪里设计。比如有时候因为序列的关系，我只能在
距离exon边缘比如20bp的地方设计一个primer。而sequencing时候的一个问题就是，刚
开始sequencing的区域的质量是很低的（比如前30bp），是不可用的。这样的话，如果
primer距离exon边缘太近，很可能exon的开头一段序列的测序质量也很低，等于说并不
是整个exon都被high-quality的测序了。。。
但是我们有两个方向，forward and reverse同时测序。所以纵然forward方向的序列很
sloppy，但reverse方向的high-quality序列可以补偿回来。
我就是想问，假设forward方向的序列很垃圾不能用，而reverse方向这个base是高质量
的，而且是reference allele，是不是就ok了，不用管forward序列了？
... 阅读全帖 |
|
j**W
发帖数: 89 | 14 因为用Ｐ３－Ｐ４做的PCR，所以做sequencing的fragment应该含GFP，不会是wildtype
allele.
但是用P1做sequencing得到"wild type sequence" (不是wildtype allele),并且都过
了该是后面的loxP的地方但是还是没看见loxP。
又不是wildtype allele，后面的loxP又不见了， 所以就只能是我图上画的mis-
targeted allele这个四不象了。
我不知道还缺什么信息。不好意思。我现在说清楚了么？ |
|
l*****0
发帖数: 299 | 15 如何说明noisy data sequence是cumulative increase的？
我在实验中获得了一个noisy data sequence. 共有50个data points. 数据值呈现
cumulative increase的趋势. 前3个数据值的累积增加很明显, 但后面的累积增加越来
越慢，淹没在noise中。请问怎样说明这一data sequence是cumulative increase的？
谢谢！ |
|
l*****0
发帖数: 299 | 16 如何说明noisy data sequence是cumulative increase的？
我在实验中获得了一个noisy data sequence. 共有50个data points. 数据值呈现
cumulative increase的趋势. 前3个数据值的累积增加很明显, 但后面的累积增加越来
越慢，淹没在noise中。请问怎样说明这一data sequence是cumulative increase的？
谢谢！ |
|
n******e
发帖数: 110 | 17 在做肿瘤RNA测序相关的研究，最近才开始注意到反转录酶的出错率，看了一些文献报
道，觉得这是个大的问题，尤其是在做一些de novo sequence 研究的时候。比如trans
-splicing 和alternative splicing，大多数开始的实验是通过cDNA来作研究的。对于
一两个的transcript到是可以用传统的方法来验证通过cDNA sequence 的结果，可是对
于高通量的测序结果，好像没有人去一个个都验证吧。下面是两篇由反转录酶引起假阳
性的例子。
有没有同学对这方面熟悉的，比如反转录酶的错误率，怎么控制RNA sequence的准确，
希望可以讨论讨论。
1. Houseley, J. and D. Tollervey, Apparent non-canonical trans-splicing is
generated by reverse transcriptase in vitro. PLoS One. 5(8): p. e12271.
2. Zeng, X.C. and S.X. Wang, Evidence that BmTXK beta-B... 阅读全帖 |
|
h*********g
发帖数: 18 | 18 I bought a pCMVsport6 vector with one gene inserted. I want to confirm the
sequence of the gene. Using T7 primers, I can get part of the sequence. But
using sp6, M13 forward and reverse primers, I cannot get any sequence. Why?
Can anyone help me about this?
Thanks. |
|
m********c
发帖数: 2 | 19 【 以下文字转载自 Immigration 讨论区 】
发信人: mayoclinic (mayoclinic), 信区: Immigration
标 题: guest editor wanted (next generation sequencing in medicin
发信站: BBS 未名空间站 (Tue Sep 2 17:31:38 2014, 美东)
大家好！Bioinformatics and Biology Insights杂志要出一本supplement，我是Next
Generation Sequencing in Medicine方向的lead guest editor。说实话杂志算不上好
，不过还算正规，毕竟被Pubmed收录。希望对感兴趣的同仁申请绿卡有帮助。
现在我需要recruit合适的guest editor。你的工作包含：1：邀约到5篇稿件；2：和其
它editors一起合写一页左右的introductory editorial。有兴趣且方向match的同仁，
欢迎站内联系我，敬请附上你的简历。
Anyone interested in worki... 阅读全帖 |
|
|
m*********D
发帖数: 1727 | 21 他science文章的protocol里是puromycin七天，然后是drug treatment七天或十四天。
要整合的话（stable cell line)，时间是该差不多了。
你说的先作Cas9的stable我要考虑一下。就是作stable cell line太花时间。Cas9的表
达silence问题该不大。一般stable在我手里是三个月之后才出现基因表达走下坡。
Lentivirus感染效率高的话，一个vector省很多事啊。上次作点突变，我用普通的
lipofectamine 3000作transfection, 效率太差，少于10%的细胞能在三天的puromycin
selection后活下来。也许我用的puromycin量太高，2.5ug/ml。当时作了一个三天的
killing，找到能三天杀完host cell的最低量，就用上了。
再向你请教一下：vector整合进genome后，拿到genomic DNA，再用primers来扩增整合
的guide Sequences。这对PCR primers 就是直接从vector来的吗？我想象这对primers
正好在gu... 阅读全帖 |
|
j******i
发帖数: 21 | 22 新人求助，第一次做miRNA deep sequencing 分析，想请问版上各位有没有比较实用的
分析protocol或者 pipeline。 还有一个问题就是， sequence read 是直接 map到
mature miRNA的 sequence上比较好，还是map 到genome上然后用 gff file locate
mature miRNA的位置。 如果是map到mature miRNA上，下一步的fold changes 的和 t
test 的分析用什么program做比较好。 菜鸟一枚，感谢赐教！！！ |
|
v********a
发帖数: 646 | 23 看到NGS Library 的制备方法里面
又是Barcode sequence ，又是index sequence
请问两者有何不同？
谢谢 |
|
k*****2
发帖数: 135 | 24 index是用来区分你的几个样品，比如你把10个样品混在一个lane里面测序（因为一个
lane的通量很大很大），又称multiplexing。
至于Barcode，比如你有100个5kb的长序列，你可以把他们分别和20bp的短序列相连，
然后通过看短序列的frequency变化反映长序列的frequency变化（这只是barcode
sequencing的一个例子，还有很多其他有趣的应用。这里需要barcode是因为你的长序
列太长了，sequencing没办法cover整个segment）。design primer的时候，两者的位
置会有不同。具体要看你要做什么问题~
呃，有点中英交杂，但是英文的部分是一般英文的用词，所以就没翻译过来啦~ |
|
g******1
发帖数: 295 | 25 email resume to arthurbuffet At hotmail dot com if interested
https://boards.greenhouse.io/guardanthealth/jobs/525188#.WEjjvrIrLIU
About the Role
We are looking for a Research Associate team member who will partner with
the successful delivery of world-class in vitro diagnostic (IVD) quality
products for Guardant Health as we undergo an explosive growth phase. You
will work closely with the R&D teams to perform laboratory experiments
including sample preparation, nucleic acid extraction, PCR... 阅读全帖 |
|
l**t
发帖数: 170 | 26 通过 n*alpha-floor(n*alpha)产生，其中n是自然数，alpha是素数
哪里可以找到关于这个sequence的paper
google不到，也不确定这个sequence就是叫alpha sequence
还是有其他的名称，多谢！ |
|
m****a
发帖数: 132 | 27 I need to have 64 orthogonal sequences, but when I use matlab as follow,
set_param('doc_ortho/Hadamard Code Generator', 'index', 'i');
the index can only be 1-63 (no matter what code generator is, hadamard,
walsh, or OVSF).
Is there any easy way to generate 64 different orthogonal sequence (not
sequence of period 64)?
Thanks in advance. |
|
m****a
发帖数: 132 | 28 I need to have 64 orthogonal sequences, but when I use matlab as follow,
set_param('doc_ortho/Hadamard Code Generator', 'index', 'i');
the index can only be 1-63 (no matter what code generator is, hadamard,
walsh, or OVSF).
Is there any easy way to generate 64 different orthogonal sequence (not
sequence of period 64)?
Thanks in advance. |
|
s*******y
发帖数: 558 | 29 Let G=(V, E) be a simple undirected graph with degree sequence d_1 >=
d_2 >= ... >= d_n, where n >= 1.
Let d_1+a_1, d_2+a_2, ..., d_n+a_n be another graphic sequence (which
is realizable). Here
0 <= a_i <= n-1-d_i , i=1, ..., n.
问题是： 如果对图G进行修改， 要求只加边不减边， 加的边是原图没有的。
有没有可能构造出一个新的simple graph， 使得其degree sequence是 d_1+a_1, ...,
d_n+a_n.
当什么情况下是可能的， 什么情况下是不可能的？
谢谢 |
|
m***b
发帖数: 11 | 30 哪儿有关于deep sequencing数据分析的tutorials, 像RNA-sequencing, methylation-
sequencing? |
|
x******a
发帖数: 6336 | 31 【 以下文字转载自 JobHunting 讨论区 】
发信人: xiaojiya (xiaojiya), 信区: JobHunting
标 题: Re: 请问longest common consecutive sequence用什么算法？
发信站: BBS 未名空间站 (Mon Jan 14 22:54:24 2013, 美东)
再请问一下，suppose两个sequences的长度都是1000，都有a,b,c,d,e五个字母构成，
每个位置是这5个字母的概率都是1/5. 那么longest common consecutive sequence的
长度期望是多少？ |
|
l*****0
发帖数: 299 | 32 如何说明noisy data sequence是cumulative increase的？
我在实验中获得了一个noisy data sequence. 共有50个data points. 数据值呈现
cumulative increase的趋势. 前3个数据值的累积增加很明显, 但后面的累积增加越来
越慢，淹没在noise中。请问怎样说明这一data sequence是cumulative increase的？
谢谢！ |
|
|
c**j
发帖数: 103 | 34 ding! Can we do it without sorting??
请问Bayesian1， 还有link没？
加个条件： 这个题如果还要要求 答案是*连续位置的*的subarray呢？
e.g.:
input: 4,5,1,5,7,4,3,6,3,1,9
sort以后1，1，3，3，4，4，5，5，6，7，9
output{5,7,4,3,6}
check careercup:
http://www.careercup.com/question?id=11256218
Microsoft Interview Question about Algorithm asm on October 19, 2011
you have an array of integers, find the longest
subarray which consists of numbers that can be arranged in a sequence, e.g.:
a = {4,5,1,5,7,4,3,6,3,1,9}
max subarray = {5,7,4,3,6}
39
http:/... 阅读全帖 |
|
m****r
发帖数: 141 | 35 Given a sequence of data (with duplicates), move a fix-sized window along
the data sequence and find mode in the window at each iteraion, where the
oldest data is removed and a new data is inserted to the window.
I cannot find better solutions here.
My idea: Use a hashtable, key is the data, key's data is the frequency of
the data occuring in the window.
At the first iteration, iterate each data in the window and put it to the
hashtable, meanwhile cout the frequency of each data. After that, tra... 阅读全帖 |
|
x******a
发帖数: 6336 | 36 再请问一下，suppose两个sequences的长度都是1000，都有a,b,c,d,e五个字母构成，
每个位置是这5个字母的概率都是1/5. 那么longest common consecutive sequence的
长度期望是多少？ |
|
g***j
发帖数: 1275 | 37 Given an unsorted array of integers, find the length of the longest
consecutive elements sequence.
For example,
Given [100, 4, 200, 1, 3, 2],
The longest consecutive elements sequence is [1, 2, 3, 4]. Return its length
Your algorithm should run in O(n) complexity.
我在网上看到了几段code，用到了set或者map，每次要在set或者map里面找到，然后删
掉，我想问，这样的code时间是n么？find in a set难道不是logn么？当然也有用到
map的，我觉得找元素都是logn啊，那么最终的时间就是nlogn啊，比如如下code
class Solution {
public:
int longestConsecutive(vector &num) {
// Start typing... 阅读全帖 |
|
m********c
发帖数: 2 | 38 大家好！Bioinformatics and Biology Insights杂志要出一本supplement，我是Next
Generation Sequencing in Medicine方向的lead guest editor。说实话杂志算不上好
，不过还算正规，毕竟被Pubmed收录。希望对感兴趣的同仁申请绿卡有帮助。
现在我需要recruit合适的guest editor。你的工作包含：1：邀约到5篇稿件；2：和其
它editors一起合写一页左右的introductory editorial。有兴趣且方向match的同仁，
欢迎站内联系我，敬请附上你的简历。
Anyone interested in working with me as a guest editor of a supplement the
journal plans to publish within the next 12 months? The topic of the
supplement is Next Generation Sequencing in Medicine.
As a guest ed... 阅读全帖 |
|
c****u
发帖数: 3277 | 39 The sequence over 1C 1H 2H
1C p 1H p 2H has been one of the toughest
sequences, because 2H covers a large
variety of hands, from SAxx HKxxx DQxx CKJx
to Sx HAKx Dxxxx CAKxxx or even Sx HAQx DAKx
CJxxxxx. How to show the
different type of hands is one of the most
challenging work in bidding.
Here, I present my new thoughts about it.
1, 2S: starts all kinds of different invitational
hands.
over 2S, opener can bid 2NT to show minimum
hands with 3 hearts, in that case, he usually
has at least 5 club |
|
w******8
发帖数: 977 | 40 在impact时hip没有clear吧，从follow through看hip turn也不够,arm outrun hip.在
impact时，hip应该face target, shoulder square。early release and chicken
wing应该也是swing sequence的问题造成的吧。这种情况下，如果不chicken wing而是
full release,很容易hook。我的感受是，如果down swing时sequence不对，右手发力
太早，就会有各种问题。 |
|
y****m
发帖数: 1322 | 41 【 以下文字转载自 NewYork 讨论区 】
发信人: yorkmm (桃之夭夭), 信区: NewYork
标 题: help with this sequence quiz,笨人请教，谢谢啦
发信站: BBS 未名空间站 (Tue Feb 7 15:00:41 2012, 美东)
人笨，请教大家一个问题，谢谢啦。
choose the anwser that best continues the sequence.
ΔΟΟΟ ΔΟΔΟ ΔΟΔΔ
a) ΔΟΟΟ b)ΔΟΔΟ c) ΟΔΟΔ |
|
r*****y
发帖数: 264 | 42 下一个sequence id应该是当前sequence的下一个值.删除当中的一条记录,不会把后面
记录的primary key往前移的.
除非是hibernate配置文件里设置了每次启动是都是重新创建table. |
|
t********k
发帖数: 808 | 43 那应该是有人自己去实现的一个类似sequence的功能
oracle的sequence不会shift的 |
|
v****s
发帖数: 1112 | 44 sty和tex文件在此：
http://nips.cc/PaperInformation/StyleFiles
sty file:
nips10submit_e.sty: style file for LaTeX 2e (preferred)
尝试编译他们提供的tex 和 sty files，但是出错。
我用的是miktex 2.9, ide 用的是texniccenter , 在lyx 1.8.6也出现同样的错误：
undefined control sequence
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
misspelled it (e.g., `\hobx'), type `I' and the correct
spelling (e.g., `I\hbox'). Otherwise just continue,
and I'll forget about whatever was undefined.
十分感谢！！ |
|
b*********t
发帖数: 877 | 45 kozac seq was found by a japanese lady whose name was kozac. she had a
single-author paper published in cell (in the 80s) describing a short
sequence around the start codon which gave rise to high level expression
in eukaryotes.
it is: ACCATGG. the "ATG" here is the start codon.
i always try to include this sequence when making plasmids for transfection. |
|
|
t********9
发帖数: 536 | 47 各位大侠，我对基因方面懂得不多，现在有一个基因方面的问题向大家请教。我想找一
个基因tag-24 的promoter sequence，这个基因是c.elegans中的。下面是有关的信息
（包括了tag-24 的一个上游基因和一个下游基因）。请大侠帮忙算一下这个promoter
sequence 是多长呢？请讲讲是怎么算的。（因为tag-24 给的是complement, 我不知道
怎么办）（就按tag-24 得第一个isoform 为例吧。）多谢了！！！
gene 5604536..5609082
/locus_tag="F14D12.1"
/db_xref="GeneID:180829"
/db_xref="WormBase:WBGene00017463"
mRNA join(5604536..5604550,5604616..5604684,5604731..5604985,
|
|
a***e
发帖数: 1010 | 48 go to wormbase.org
search tag-24
go to "location", click the picture, "Showing 2.515 kbp from X, positions 5,
608,905 to 5,611,419"
in "landmark or region", change "X:5608905..5611419" to "X:5608905..5613419"
In "reports & analysis", change to "download sequence files", click "go"
it will give you the 2k promoter plus the whole gene sequence. |
|
t********9
发帖数: 536 | 49 Arche. I think I know why I need to change the number.This way it will give
me 2 kb promoter sequence. Thanks!!!
However, do you or anyone know how to figure out the promoter sequence based
on the information from pubmed.com as I pasted in the first message? |
|
t********9
发帖数: 536 | 50 ahche, why I can not find the tag-24 gene sequence from the "2k promoter
plus the whole gene sequence"? tag-24 gene starts with atgtggaaccttaactg.....
5,
5613419" |
|
