http://www.protocol-online.org/forums/index.php Fri, 20 Nov 2009 16:23:06 -0800 360 http://www.protocol-online.org/forums/index.php?showtopic=11684 Thu, 19 Nov 2009 16:12:49 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11684 http://www.protocol-online.org/forums/index.php?showtopic=11651
i've got a blastn xml-output file from a bioinformatic and i'm now looking for a programm able to visualize this xml-output file. I've tried blast2go, but it gives me no information on the sequence and i want to see the different sequences aligned to each other, like in the web blast output. What's the programm of choice for such a task? I've no clue?

Many thanks in advance for your help!

Regards,
p]]> Wed, 18 Nov 2009 12:34:51 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11651 http://www.protocol-online.org/forums/index.php?showtopic=11639
I have got a problem. I did PCR and sequencing of nuclear Internal Transcribed Spacer (ITS) of a plant using two primers ITS1(forward) and ITS4 (reverse) . The PCR was quite successful. I employed the same primers for sequencing reaction and got two clean sequences (forward and reverse) without secondary peaks. I used the SEQUENCHER software to make the consensus sequence, however, the forward and reverse sequences appear in the same direction. Why the sequences obtained from forward and reverse primers didn't run in opposite directions in sequencher? PLEASE HELP. Thank you in advance!!!!!!

Sincerely,
]]> Wed, 18 Nov 2009 04:18:51 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11639 http://www.protocol-online.org/forums/index.php?showtopic=11631
thanx]]> Tue, 17 Nov 2009 21:00:41 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11631 http://www.protocol-online.org/forums/index.php?showtopic=11630 I want to search whether a particular inverted repeat sequence present in the promoter region of E.coli gene is also present in other species of bacteria. Since it is just a 20bp long region, I dont know how to use NCBI blast option sad.gif guide me pls rolleyes.gif . I thank all of you..




Abhay]]> Tue, 17 Nov 2009 20:00:01 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11630 http://www.protocol-online.org/forums/index.php?showtopic=11628 I want to search whether a particular inverted repeat sequence present in the promoter region of E.coli gene is also present in other species of bacteria. Since it is just a 20bp long region, I dont know how to use NCBI blast option guide me pls . I thank all of you..




Abhay]]> Tue, 17 Nov 2009 19:56:42 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11628 http://www.protocol-online.org/forums/index.php?showtopic=11626 how to find intron exon location in plant dna? Tue, 17 Nov 2009 18:18:03 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11626 http://www.protocol-online.org/forums/index.php?showtopic=11584
does anyone know a software solution to the storage of sequencing files. I always have problems with handling them because you download them and put it in a directory but after a while hundreds of them are accumulating and if you are looking for a spcific one after a while its like searching a needle in the haystack! Is there a prog like for example itunes to handle sequencing files?

Many thanks in advance!

Regards,
p]]> Mon, 16 Nov 2009 14:03:27 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11584 http://www.protocol-online.org/forums/index.php?showtopic=11504
i want to know ,is there any program or software available on net , which can tell u about interactions among receptor and its corresponding legend.

which can tell about bond formation or interaction that happened during receptor and legand interaction.

i will be thankfull .
]]> Thu, 12 Nov 2009 20:41:59 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11504 http://www.protocol-online.org/forums/index.php?showtopic=11484
Yet another quick question! Can anyone tell me if the Xenopus genome is fully annotated yet?

Kami]]> Thu, 12 Nov 2009 03:26:26 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11484 http://www.protocol-online.org/forums/index.php?showtopic=11435
I know that for a model 1 ( fixed ) anova, it is meaningful to perform multiple comparisons ( like Tukey test ) and that for a model 2 ( random ) anova, it is not meaningful to perform multiple comparisons.

I would like to know for a model 3 ( mixed ) anova if it is meaningful or not to perform multiple comparisons.

Thank you very much ]]> Mon, 09 Nov 2009 20:10:25 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11435 http://www.protocol-online.org/forums/index.php?showtopic=11372 Does some body knows how to draw a phylogenetic tree of any family.... Thu, 05 Nov 2009 02:17:10 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11372 http://www.protocol-online.org/forums/index.php?showtopic=11363 I just constructed a genetic map for cowpea and want to draw a synteny map with the published model legume genetic map.
many published documents contain some very beautiful syteny map but I don't know how to make such a map? by hand or there are already softwares to aid this?
Thanks very much for any of your answers!
Blessings!]]> Wed, 04 Nov 2009 22:39:41 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11363 http://www.protocol-online.org/forums/index.php?showtopic=11359
Could someone guide me through this question plese?

http://mathbin.net/36011

what type of anova should I perform? It looks like a 3 factor anova, but i'm not sure if i'm on the right track.

Any help would be appreciate, thanks ]]> Wed, 04 Nov 2009 16:12:13 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11359 http://www.protocol-online.org/forums/index.php?showtopic=11346
Thanks in advance,

Kami]]> Wed, 04 Nov 2009 06:43:25 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11346 http://www.protocol-online.org/forums/index.php?showtopic=11339 I have 20 samples and 4tests each. How can I present it in my paper? I tried the bar chart, but it seems that my samples are too many to be presented clearly.
I have found the attached chart but I donot know how to draw it.
any suggestion?
Many thanks in advance]]> Wed, 04 Nov 2009 03:19:56 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11339 http://www.protocol-online.org/forums/index.php?showtopic=11325
I'm having a hard time with all the different type of anova test and I'm stuck on a particular question, where I think, there is many possible answer.

http://mathbin.net/35930

so basically depending on if you think if there are others interaction, and that you can't test them, you could do :

Model I two factor anova
Model II two factor anova
Model III two factor anova
or also
Nested anova
Split-plot test

Personaly, if I understand well, I would go with a Model II two factor nested anova, does it make sense? Or there is just one possible test for this particular situation?

Any help would be greatly appreciated, thank you ]]> Tue, 03 Nov 2009 11:35:19 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11325 http://www.protocol-online.org/forums/index.php?showtopic=11312 what is the best tools for promoter detection and analysis? Mon, 02 Nov 2009 23:35:01 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11312 http://www.protocol-online.org/forums/index.php?showtopic=11311
Anyone has qBase freeware? Would appreciate it if I can get a hold on it for qPCR calculation. I tried downloading the qBasePlus at http://www.biogazelle.com/ but the link seemed to take like forever to load.

Would appreciate it if you can direct me to a new site to download (if the above site is no longer available)

Thanks.]]> Mon, 02 Nov 2009 23:17:51 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11311 http://www.protocol-online.org/forums/index.php?showtopic=11281

How to find the DNA sequence [-2000, +2000] relative to TSS and
[+2001, end of gene] for
1) L44140 COMT gene in human chromosome 22
2) X52828 BCR gene in human chromosome 22

Can some one help me...

Thanks,
Arniker]]> Sun, 01 Nov 2009 03:02:31 -0800 http://www.protocol-online.org/forums/index.php?showtopic=11281