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...
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...
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...
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...
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 ...
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/...
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. ...
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...
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...
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...
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...
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...
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...
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? ...
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 ...
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...
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...
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...
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: ...
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...
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: ...
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...
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...
48
ssahausers@...
Oct 16, 2005 12:42 pm
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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...
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...
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...
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...
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...
54
diva.bensley1717@...
Jan 15, 2006 4:16 pm
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...
