Just thought I should pass on my knowledge to all you guys (and gals) on here. I know just like heaps of other men I am pretty shy when it comes to going up to...
53
Conrad Halling
chhalling
Jan 12, 2006 10:59 pm
SSAHA users, This is a follow-up to my post on December 29, 2005, about patching SSAHA 3.1 so it will compile using the GCC 4.0.1 compiler. I finally got...
52
Conrad Halling
chhalling
Dec 30, 2005 1:26 am
SSAHA users, I attempted to compile SSAHA 3.1 on my Mac OS X computer using the latest compiler, GCC 4.0.1. Unfortunately, GCC 4.0.1 is much more finicky about...
51
diva.bensley1717@...
Dec 28, 2005 5:00 am
Thought Id share something with ya'll. Great fun and it actually works. Met my girl on here, http://www.findawife.info/dzjy and so far it's been the best...
50
Adam Spargo
a_w_spargo
Nov 28, 2005 9:37 am
Hi, The algorithms are very simple. The key set is very small (when compared to the sequence data). We map ALL kmers whether they appear in the sequence or...
49
greenexile4568
Nov 28, 2005 1:44 am
Hi, Is there a pseudocode representation of the SSAHA algorithm ? I'm particulary interested in learning what approaches were taken to implement the various...
48
ssahausers@...
Oct 16, 2005 12:42 pm
Global Triad, Inc: (OTC: GTRD - Breaking News) Trading symbol: GTRD Current Price: .036 Target Price: .150 Expected Short Term Gain: 400 percent Rating: 10 out...
47
Adam Spargo
a_w_spargo
Sep 2, 2005 8:39 am
Hi, Unfortunetly there is nothing online yet, but usage is straigth-forward. A man page and an example is enclosed in the download, please feel free to contact...
46
Cook, Malcolm
malcookmalcook
Sep 1, 2005 4:51 pm
I'm wondering if there is some documentation available on-line - especially regarding ssaha2est. regards and TIA, Malcolm Cook...
45
Adam Spargo
a_w_spargo
Sep 1, 2005 4:35 pm
We are pleased to announce a new release of the ssaha2 package along with the first release of ssahaEST. You can download binaries at: ...
44
euclidean253@...
euclidean253
Oct 18, 2004 6:19 am
We invite you to join the free World Science news list! To subscribe for free, just send an email here: emailnews@... and type “subscribe” in...
43
pauline_ng_98105
pauline_ng_9...
Dec 12, 2003 4:07 am
Hello, Has anyone ever successfully run testHashTableNoOverlap on Windows? Tests 1-6 are completed successfully, but in Test 7 I'm getting an exception: ...
42
malcookmalcook
Dec 2, 2003 10:25 pm
I am trying to prove my understanding of SSAHA prior to using it for analysis but it is not working as I expect. From the Ensemble Tracer Server, I find the...
41
Will Spooner
whs_qwghlm
Jun 12, 2003 8:19 am
... Yes - this is expected, and is a result of the SSAHA method: When SSAHA starts, a lookup table is constructed of all possible DNA combinations for a given...
40
Altaf Kassam
kassaal
Jun 4, 2003 9:41 pm
I get the following error while attempting to build the Ensembl Client/Server binaries. I was unsuccessful in building the ssaha binary on this machine, so I...
39
jlim1197
Apr 18, 2003 12:04 am
Interestingly, I came across a perl interface for the non-client/server binary. It's part of the Ensembl-Pipeline package ...
38
mccon012
Apr 17, 2003 4:39 pm
testSequenceReaderFasta fails on irix 6.5 with g++ 3.0.4. The output is posted below. SequenceReaderFasta appears to chop 1 base off the end. Any ideas? ...
37
Will Spooner
whs_qwghlm
Apr 17, 2003 9:28 am
... Hmm, this is a bit tricky. The client/server builds fine using gcc on tru-64, but won't build cleanly under Linux. I've fixed a few bits, but have hit my...
36
jlim1197
Apr 16, 2003 8:49 pm
I'm having problems compiling the code under various machines. Has anyone been able to compile successfully under x86 linux and Sun Solaris? Will there be...
35
Will Spooner
whs_qwghlm
Apr 16, 2003 1:33 pm
I'm pleased to announce the availability of SSAHA v3.1. This is a minor release that addresses several platform compatibility issues. The complete C++ source...
34
Will Spooner
whs_qwghlm
Apr 16, 2003 12:30 pm
Hi Naohisa, That's a great help! Seems to have cleared up all those pesky command-line-option bugs under linux. You've prompted me to combine a few fixes I've...
33
Will Spooner
whs_qwghlm
Apr 16, 2003 7:49 am
... No, this is the standalone ssaha executable. ... You'll need to download the source code (ssaha_v30.tar.gz). There are instructions on building the...
32
ngotogeninfo
Apr 16, 2003 7:43 am
Hi, I made a patch for ssaha_v30.tar.gz. It seems working fine on Debian/GNU Linux 3.0 (gcc 2.95.4 and 3.0.4). Patch to Global/GlobalDefinitions.cpp fixes a...
31
jlim1197
Apr 15, 2003 6:46 pm
The only file I can find on the website is ssaha_v30_linux. Is this the file that I can run as a server process? If not, can someone provide the link? Thanks. ...
30
jlim1197
Apr 15, 2003 6:21 pm
Thanks for the tip. I will give that a try. ... server on ... http://docs.yahoo.com/info/terms/...
29
Will Spooner
whs_qwghlm
Apr 15, 2003 7:56 am
Hi Jonathan, Unfortunatly there is currently no Perl API to SSAHA. However, if you're building a web interface, you may like to look at the EnsemblServer ...
28
jlim1197
Apr 14, 2003 5:09 pm
Hi there, I'd like to integrate a SSAHA search into a web-based gene annotation system (using Perl) that I'm developing. Just wondering if there's an API or...
27
Ken
keng9675386
Mar 18, 2003 6:01 pm
Thanks for the reply. I hope to start working with this project in a month. I'm sure you'll hear from me again once I actually start ;) Thanks again, Ken...
26
Will Spooner
whs_qwghlm
Mar 18, 2003 12:24 pm
We're also considering using SSAHA for primer analysis. The main problem is SSAHA's sensitivity for exact-matching short sequences. The important parameters...
25
keng9675386
Mar 14, 2003 8:58 pm
Is SSAHA suitable for searching genomic sequences using PCR primers (i.e. 15 to 30mers) as the querys? I'll have a couple hundred primers that I'll need to...
