t*****z
发帖数: 1598 | 1 我在搞大规模BLAST以确定基因组测序片段的物种归属等问题，现在的NCBI nr数据库已
经有40GB以上，在自家电脑上做BLAST效率很低。我经过反复摸索，发现了一条诀窍：
把数据库放在SSD上，效率会提高一个数量级！但是即便如此，因为要测的序列多，整
体效率还是不理想。所以我想向大家求助，有什么更快的方法：
目前想到几个：
1）有没有可能把整个BLAST数据库都读到内存里？我观察BLAST时的内存占用率，似乎
远远没有占满，看来程序（ncbi-blast+）并没有充分利用内存？
2）一次提交多个查询序列，会比较快吧？
3）找BLAST的替代品。我已经试过GPU-BLAST，花了两天终于测试成功了。但是速度比
原始BLAST还要低！我的显卡已经超高级了，不该这样啊。还有些BLAST以外的算法，比
如Usearch，不知道业界认可程度怎样。
4）利用学校里的超算。我不知道这样能否加速，超算固然CPU核心多，但是如果BLAST
的瓶颈在于I/O，那么超算恐怕也不如我的装备了SSD的家用电脑快。
各位有什么想法呢？多谢！ |
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m**********n
发帖数: 27535 | 2 BEIJING – China joined the world in breathless coverage of the Chilean mine
rescue, but when a gas blast killed 21 Chinese miners and trapped 16
Saturday, the national TV evening news didn't say a word. Rescuers said they
were fighting tons of coal dust to reach the miners, who have been located
but whose condition was unknown.
The rescuers also faced dangerous gas levels and the risk of falling rocks
as they worked their way into the mine pit.
The early-morning explosion in central China happen... 阅读全帖 |
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b*********s
发帖数: 6757 | 3 ５）问题１：听说这个线只能达６－８小时，是这样的吗？A dead bed 会很不一样吗
？那么贵，我打算打起码２０小时，可行吗？
--这得看你和你用的拍子。 我觉得一般来说20小时该可行的， 有些人半年才打断
RPM blast, 有些人1 星期。 这得自己试试了。我用RPM Blast 的感觉是， fresh
strung feels great, 打了一会 （maybe 1 match), 就一般了。 当线“快”断时，
it feels dead, 但又不忍心剪， 继续下去可能却还能打半小时， 1个set左右。。。
。 我个人比较喜欢tourna BHB7, 便宜， 但没有rpm blast 耐用， 但当感觉线快断时
， 基本1～2个game or 5~10min more rally线就断了。
６）问题２：有没有谁用过RPM Blast and Gosen Polylon? 有比较吗？Gosen Polylon
很便宜，评价也不错，＄３５一个reel,只能买２个RPM Blast.如果感觉差不多的话，
可能是长期的选择。
--前段时间试用过volkl cyclone 感觉还不错... 阅读全帖 |
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g*r
发帖数: 67 | 4 可以在自己电脑上安装blast程序。有一个选项“-remote”可以用来检索ncbi网站的数
据库。虽然query依然是有限制，但你可以把大文件分成小块，分别提交任务。remote
模式依赖远程服务器，并受网络状况影响。有时会遇到超时、掉线、没反应等问题，你
检查结果发现后可以重新提交哪些没完成的序列。个人感觉remote的速度很不理想。
如果你序列很多或者用得比较频繁，可以考虑下载ncbi的database（比较大，起码几十
G，但对当今的硬盘来说小菜一碟）。local blast速度快，想怎么blast就怎么blast。 |
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w*******y
发帖数: 60932 | 5 Lara Croft and the Guardian of Light-Xbox 360[Digital Download]:
http://www.bestbuy.com/site/Lara Croft and the Guardian of Light-Xbox 360[Digital Download]/1000001021.p?id=1000001020&skuId=1000001021&st=lara croft&lp=1&cp=1
- $5
Galaga: Legions-Xbox 360[Digital Download]:
http://www.bestbuy.com/site/Galaga: Legions-Xbox 360[Digital Download]/1000001191.p?id=1000001190&skuId=1000001191&st=galaga&lp=2&cp=1
- $5
Call of Duty: Resurgence Pack-Xbox 360[Digital Download Add-On]:
http://www.bestbu... 阅读全帖 |
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G***G
发帖数: 16778 | 6 two days ago, when the first blast happened on
reactor no.1. People explained that it was because of
power outrage and generator broken by tsunami.
did people ship a new generator to there? no reports about it.
did people fix the power outrage? no reports about it.
but shipping a generator or fixing the power outrage
should be a easy task.
now the third blast happened.
people began to ask ,' when the first blast happened,
it was really caused only by power shortage or broken generator?
most poss... 阅读全帖 |
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M******0
发帖数: 1280 | 7 第一次换上polyster的网线，RPM Blast, ５３磅，打了１个半小时。一点小体会，加
几个小问题。
１）Control,很棒，终于可以用尽力气拉和抽，怎么也不出界。以前用的都是１，２块
钱的尼龙线，发力总是有所保留。昨天整整发力打了１个半小时，对面的球友很不适应
，我整晚直下４盘。
２）Spin,明显容易且强大很多
３）Power,也许是tension 较低，没有明显的reduction,反而我能自己发力，球more
powerful.
４）没有觉得任何手腕或elbow的不适。我以前打便宜的线是道是有几次手腕的不适。
不只为什么说对elbow 回不好？
５）问题１：听说这个线只能达６－８小时，是这样的吗？A dead bed 会很不一样吗
？那么贵，我打算打起码２０小时，可行吗？
６）问题２：有没有谁用过RPM Blast and Gosen Polylon? 有比较吗？Gosen Polylon
很便宜，评价也不错，＄３５一个reel,只能买２个RPM Blast.如果感觉差不多的话，
可能是长期的选择。 |
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l**********1
发帖数: 5204 | 8 >回复]
[ 1 ]
发信人: thomasz (thomasz), 信区: Biology
标 题: ？怎样Blast较大的序列？
发信站: BBS 未名空间站 (Sat Feb 25 14:36:17 2012, 美东)
我有个6.6kb的DNA序列，是某个细菌基因组中的一段
。但是我
知道别的基因组里确实有整段的同源序列的。想来6.6kb也不是很大，那该怎么做好呢
？多谢！
----
and
cited:
------------
出一大堆 somewhat similar to Optimize for Somewhat similar sequences by (blastn)
then what is the next step?
Fishing most important hits?
//www.ncbi.nlm.nih.gov/blast/Blast.cgi?
CMD=Web&LAYOUT=TwoWindows&AUTO_FORMAT=Semiauto&ALIGNMENTS=50&ALIGNMENT_VIEW=Pairwi
se&
CLIENT=web&DATA... 阅读全帖 |
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C***U
发帖数: 2406 | 9 不好意思
我是从那个网页下载的
更细的链接是这个
ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
那个网页确实是网上的blast
是我没说清楚 |
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t*****z
发帖数: 1598 | 10 各位，我已经尝试了在超算上跑多个BLAST。确实每个节点都不算快，但是多个任务一
起跑效果明显。同时我发现，装备了四路E7处理器共32核心的节点跑BLAST飞快，速度
10倍于我的个人电脑。我也不知道为什么。推测内存数据读取的速率可能是个重要的瓶
颈。四路E7节点装备了4x4=16通道DDR3内存，远高于一般个人电脑的2-4通道，所以有
如此显著的效果。这个节点全校只有个位数，很难轮到，所以也无法指望。
我也在自己实验室的工作站上试验。该机器硬盘速率很低，但是内存速率较高（2x3=6
通道）。如果每次只输入一个待查询的序列，那么速度很慢；但是如果每次输入二三十
个序列，速度立马就上去了，抵得过装备了SSD的个人电脑。同时，在个人电脑上尝试
这一招，是没有明显效果的。这进一步支持了我关于I/O是BLAST效率瓶颈的推测。 |
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n******n
发帖数: 1030 | 11 在electronic transformer周围搞个fire/blast wall,这个fire还可以看看NFPA 850
但是blast load就太难搞定了，有人说UL STANDARD 750,这个有同学有吗？
Military Code也好像没说太详细的，做过的大侠给指导一下吧，小项目，不可能买什
么专业软件搞blast analysis.
就像找个简单公式算算。
多谢了。 |
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w*******y
发帖数: 60932 | 12 Kohls.com has the Banzai Splash Blast Water Slide marked down to 299.99
originally 499.99 after 30% coupon(Charge Customers Only) and Kohls Cash
this comes to 169.99 plus tax.
This price is the lowest I have seen on a slide that is this big! Next
lowest price I have seen was 399.95. This would be great for the kids this
summer!
Link:
Link:
http://www.kohls.com/kohlsStore/toys2009/shopbyage/67/PRD~80796 Splash Blast Water Slide.jsp
Banzai turns your backyard into a waterpark. With its climbing wa... 阅读全帖 |
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l*****7
发帖数: 8463 | 13 Germany blasts Britain
See the link below:
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
http://www.guardian.co.uk/uk/2013/jun/25/germany-uk-gchq-intern
Germany blasts Britain over GCHQ's secret cable trawl
Minister questions legality of mass tapping of calls and internet and
demands to know extent to which Germans were targeted
Cameron and Merkel
David Cameron and Angela Merkel. The German government's letter is the first
major challenge to the UK over its data-trawling opera... 阅读全帖 |
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s*******u
发帖数: 476 | 14 【 以下文字转载自 Military 讨论区 】
发信人: veggie (走位飘忽), 信区: Military
标 题: Airborne Boeing laser blasts ground target
发信站: BBS 未名空间站 (Thu Sep 3 17:53:55 2009, 美东)
摘要 12000lb重的机载化学激光器射了一次，轰了（蒸发了？）地面上的一个车辆。
Zapping things from the sky: Airborne Boeing laser blasts ground target
Boeing and the US Air Force today said that they fired Boeing’s Advanced
Tactical Laser at a ground target.
By Layer 8 on Tue, 09/01/09 - 3:51pm.
C-130The airborne military laser which promises to destroy, damage or
disable targets w |
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D*V
发帖数: 3096 | 15 Germany blasts Britain
See the link below:
<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
http://www.guardian.co.uk/uk/2013/jun/25/germany-uk-gchq-intern
Germany blasts Britain over GCHQ's secret cable trawl
Minister questions legality of mass tapping of calls and internet and
demands to know extent to which Germans were targeted
Cameron and Merkel
David Cameron and Angela Merkel. The German government's letter is the first
major challenge to the UK over its data-trawling opera... 阅读全帖 |
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t*******e
发帖数: 2113 | 16 教主现在百无禁忌啊！
http://www.nypost.com/seven/07012008/news/nationalnews/barack_blasts_moveon_117949.htm
BARACK BLASTS MOVEON
HITS LEFTY PALS OVER 'GENERAL BETRAY US'
By CHARLES HURT in Washington, DC, and CARL CAMPANILE in NY
Barack Obama yesterday landed a right hook on one of his biggest left-wing
supporters yesterday - blasting MoveOn.org for labeling Gen. David Petraeus
"General Betray Us."
Obama, in a patriotism speech in Independence, Mo., hit the Web site for
taking out an ad in The New York Ti |
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l****z
发帖数: 29846 | 17 Game Over: WI Supreme Court reinstates collective bargaining law, blasts
activist judge
Jun 15, 2011
Late yesterday, the rule of law won, judicial activism lost. The Wisconsin
Supreme Court blasted a lower court activist judge from legislating from the
bench, and reinstated the union law passed by the legislature and signed
into law by Governor Scott Walker. From JS Online via memeorandum: Supreme
Court reinstates collective bargaining law
Acting with unusual speed, the state Supreme Court on Tu... 阅读全帖 |
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l****z
发帖数: 29846 | 18 By RUSSELL CONTRERAS, Associated Press
December 6, 2011
ALBUQUERQUE, N.M. (AP) — A severe winter blast has struck most of New
Mexico, closing hundreds of schools and shutting down major highways across
the state.
Motorists sought emergency shelter overnight as state officials closed both
directions of Interstate 40 from Albuquerque to Gallup — part of the
historic Route 66 — after blowing snow caused near-zero visibility.
Authorities also shut down the state's entire length of Interstate 10, fro... 阅读全帖 |
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g********d
发帖数: 4174 | 19 【 以下文字转载自 QueerNews 讨论区 】
发信人: globalized (麻球), 信区: QueerNews
标 题: APA Blasts Allegedly Biased Report on Gay Parents
发信站: BBS 未名空间站 (Thu Jun 14 17:08:17 2012, 美东)
http://www.apa.org/news/press/response/gay-parents.aspx
A recent study called into question the ability of gay parents to raise well
-rounded children, but the report has been widely blasted as biased,
manipulative, and agenda-based. Now the American Psychological Association
has stepped in to reiterate its belief that gay parents are... 阅读全帖 |
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i********f
发帖数: 206 | 20 有人用这个BLAST+的新版本么？
里面-entry和-entry_batch的参数是怎么设的？
-entry除了all可以用，自己输序列名字，好像不行啊。
序列
>chr01
CCCTAAACCCTAAACCCTAAACCCTAAACCTCTGAATCCTTAATCCCTAAATCCCTAAATCTTTAAATCCTACATC
CAT
命令行:
blastdbcmd -db SEQ -dbtype nucl -entry chr01 -range 70-75 -strand plus -out
outfile
这个报错BLAST query/options error: No valid entries to search
有人碰见类似问题的么？多谢 |
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A*******e
发帖数: 284 | 21 请教，我想了解一个基因的表达情况，所以blast geo database，得到了一个结果。结
果是一个柱图，有高低柱子。 请问GEO blast的结果到底怎么解释？ 那个“E" 链接进
去就一个结果。我敢肯定的是这个物种做了上万的microarray，为什么就给我一个试验
结果，这个E链接进去的结果用什么cutoff的，表达水平吗？ 如果我只有一个结果，是
这个gene在已知的试验条件，或者说所有的microarry里表达水平都不怎么变化吗？多
谢多谢！ |
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C***U
发帖数: 2406 | 22 I am using NCBI BLAST, here it is
http://blast.ncbi.nlm.nih.gov/
in the document, it says it takes 11 as default value for word size.
Thanks.
use |
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g**********t
发帖数: 475 | 23 I am a little bit confused. you said you used the local blast but the link
is the online version. anyway the default nucleotide blast (online) is
optimized for highly similar sequences (megablast) . be sure you used the
correct setting. |
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r******y
发帖数: 21907 | 24 用了NCBI，但是我的sequence file太大了，30M多，人家不给算，有什么可以下载用于
自己电脑blast的软件，而且可以用PHI-BLAST的？或者哪个网站能做>30M的文件的？谢
谢！ |
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w*******y
发帖数: 60932 | 26 I got this in the mail yesterday. Comcast is currently offering their Blast
internet (16Mbs to 20Mbs down) plus basic cable for $29.99 FOR BOTH each
month for 12 months.
Normally the Blast internet is $57.95 and basic cable is $21.15, which
totals $79.10. This deal saves you $49 per month.
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r**m
发帖数: 2823 | 31 Paris attacks: At least 149 killed in gunfire and blasts, French official
says |
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g********d
发帖数: 4174 | 32 http://www.apa.org/news/press/response/gay-parents.aspx
A recent study called into question the ability of gay parents to raise well
-rounded children, but the report has been widely blasted as biased,
manipulative, and agenda-based. Now the American Psychological Association
has stepped in to reiterate its belief that gay parents are just as good as
straight parents.
"On the basis of a remarkably consistent body of research on lesbian and gay
parents and their children, the American Psychologic... 阅读全帖 |
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n*********n
发帖数: 1534 | 33 【 以下文字转载自 ChinaNews 讨论区 】
发信人: qilikala999 (qilikala), 信区: ChinaNews
标 题: As Olympics protests mount, China blasts its foreign critics
发信站: BBS 未名空间站 (Wed Apr 16 01:36:38 2008)
http://news.yahoo.com/s/mcclatchy/20080415/wl_mcclatchy/2910500
By Tim Johnson, McClatchy Newspapers
Tue Apr 15, 3:41 PM ET
BEIJING — Bristling at criticism in the run-up to the Summer Olympics,
China is lashing back at its foreign critics— by name.
Earlier this week, the state Xinhua news agency called House Speaker Nan |
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s*****n
发帖数: 5488 | 34 【 以下文字转载自 Investment 讨论区 】
发信人: slimcan (周易炒股好), 信区: Investment
标 题: blast is pretty accurate in this article
发信站: BBS 未名空间站 (Sat Nov 22 00:16:05 2008), 转信
We don't need it now. but this is good one.
Struggling Stocks, Booming Commodities
04/28/2005
NASDAQ dropped -12.5% year to date in 2005. S&P500 index suffered -5.7% this
year. US stock market has been terrible over past few months.
Not only general market is down, oil stocks recently had a significant
correction as well. It is easy to be n |
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b******y
发帖数: 9224 | 35 I know a bunch of email blast services. If anyone interested, please PM me
as I don't want to be perceived as doing advertisement here. |
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b******y
发帖数: 9224 | 36 另外，只用email blast软件，是不够的。因为很多大的isp，比如说Google, Yahoo等
，会对不良的email sender有禁止的。有想了解详细的，可以站内进一步交流. |
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g********s
发帖数: 82 | 37 【 以下文字转载自 Investment 讨论区 】
发信人: samovar (sam), 信区: Investment
标 题: 好戏才开始:Ore. bank blast kills police officer, bomb expert
发信站: BBS 未名空间站 (Sat Dec 13 22:07:01 2008)
WOODBURN, Ore.—A bomb explosion at a bank killed both a police officer and
a state bomb disposal technician, and state police do not have any suspects,
officials said Saturday.
"That person is dangerous and needs to be found as soon as possible," said
Oregon State Police Lt. Gregg Hastings.
The explosion occurred Friday afternoon at |
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p****g
发帖数: 355 | 38 我曾经被service劝着上了这个blast+电视,到取消/降级的时候就告诉你是一签2年的，
要early termination fee. |
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j**n
发帖数: 94 | 40 Guys,
When you drive your ball into the trees, what club do you choose to blast it
out back to the fairway? (assuming it doesn't allow you a shot to the
green)
What is your technic to hit a low cut shot? How do you control the distance
to make sure it flies long enough to land on fairway but not too long so it
goes into the other side of trees? |
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z*********n
发帖数: 94654 | 41 我最近两周都在用这个线，教练的拍子，他上的rpm blast 16，我觉得感觉挺好的，很
实在。借给我的时候教练就挑得他的打的最久的一个拍子给我的，我这俩礼拜打得也超
频繁，结果线好像的确没啥变化，很耐 |
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M******0
发帖数: 1280 | 42 Just checked in TW, tourna BHB7 $9.99, Volkl cyclone $7.99, much better
price than RPM blast $17.99. Gonna try them.
Polylon |
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l****y
发帖数: 293 | 43 理由：转载毫无意义的评论，有灌水之嫌。
如blast不服，可到sysop申诉。 |
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e*e
发帖数: 38 | 44 这灌水的人还多着呢. 包括许多当官的. 就许州官放火,不许百姓点灯?
况且BLAST 转的并不见得就毫无意义, 倒是某些人东扯西扯的无聊有灌水之嫌 |
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p***s
发帖数: 90 | 45 COMCAST BLAST ! internet service 的 speed 是多少呀? 我现在用Docsis 2.0
Modem
用upgrade 到Docsis 3.0 Modem 吗? 谢谢. |
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k****5
发帖数: 546 | 46 blast 说有 Downloads up to 20Mbps, uploads up to 4Mbps with PowerBoost
fios : Download up to 15 Mbps/Upload up to 5 Mbps
实际情况如何？有用过的同学吗？ |
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Z**R
发帖数: 1233 | 47 NASA's new planet-hunting Kepler telescope launched into space late Friday,
lighting up the night sky above Florida as it began an ambitious mission to
seek out Earth-like planets around alien stars.
Kepler blasted off atop a Delta 2 rocket from the Cape Canaveral Air Force
Station in Florida at 10:49 p.m. EST (0349 March 7 GMT). The $600 million
spacecraft will gaze at a single region of our Milky Way galaxy for at least
three years in a planetary census that, scientists say, could fundamentall |
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p**h
发帖数: 99 | 48 free, pc.
Basic Alignment Search Tool uses amino acid fragements and nucleic acid fragments to
search for similarities
ftp://ncbi.nlm.nih.gov/blast/executables/ |
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