Short Sequence Blastn question - (Apr/24/2007 )
I'm trying to search the VZV genome for locations of a short 5 base sequence and I'm having trouble getting the blast to work for me.
I've read the help file and adjusted the parameters the best I can, but it seems to me that a 5 base sequence is just too small to blast (7 is minimum?). I'm aware that this sequence will get many hits. Any suggestions? Thanks.
Kris
-kmwpup-
QUOTE (kmwpup @ Apr 24 2007, 11:55 AM)
I'm trying to search the VZV genome for locations of a short 5 base sequence and I'm having trouble getting the blast to work for me.
I've read the help file and adjusted the parameters the best I can, but it seems to me that a 5 base sequence is just too small to blast (7 is minimum?). I'm aware that this sequence will get many hits. Any suggestions? Thanks.
Kris
I've read the help file and adjusted the parameters the best I can, but it seems to me that a 5 base sequence is just too small to blast (7 is minimum?). I'm aware that this sequence will get many hits. Any suggestions? Thanks.
Kris
What is VZV genome? How big is it?
If it is small, just use a text editor to search for the 5 base sequence, u are looking at an exact match anyway.
The best way to do it is to write a perl program. Just 5-6 line of code should do it.
-cyberpostdoc-
QUOTE (cyberpostdoc @ May 2 2007, 05:44 PM)
QUOTE (kmwpup @ Apr 24 2007, 11:55 AM)
I'm trying to search the VZV genome for locations of a short 5 base sequence and I'm having trouble getting the blast to work for me.
I've read the help file and adjusted the parameters the best I can, but it seems to me that a 5 base sequence is just too small to blast (7 is minimum?). I'm aware that this sequence will get many hits. Any suggestions? Thanks.
Kris
I've read the help file and adjusted the parameters the best I can, but it seems to me that a 5 base sequence is just too small to blast (7 is minimum?). I'm aware that this sequence will get many hits. Any suggestions? Thanks.
Kris
What is VZV genome? How big is it?
If it is small, just use a text editor to search for the 5 base sequence, u are looking at an exact match anyway.
The best way to do it is to write a perl program. Just 5-6 line of code should do it.
Thanks for the response. Its only 125kb so I did attempt the text search, but due to the formatting of the sequence it was difficult.
What I eventually did was search for a 7bp sequence in a blast, just using every combination of the 4 bases to comprise the in the 2 bases tagged on the the 5bp sequence I was interested in.
-kmwpup-
QUOTE (kmwpup @ May 10 2007, 01:32 AM)
<br /><br /><br />Thanks for the response. Its only 125kb so I did attempt the text search, but due to the formatting of the sequence it was difficult.<br /><br />What I eventually did was search for a 7bp sequence in a blast, just using every combination of the 4 bases to comprise the in the 2 bases tagged on the the 5bp sequence I was interested in.<br /><br /><br /><br />
QUOTE (cyberpostdoc @ May 2 2007, 05:44 PM)
QUOTE (kmwpup @ Apr 24 2007, 11:55 AM)
I'm trying to search the VZV genome for locations of a short 5 base sequence and I'm having trouble getting the blast to work for me.<br /><br />I've read the help file and adjusted the parameters the best I can, but it seems to me that a 5 base sequence is just too small to blast (7 is minimum?). I'm aware that this sequence will get many hits. Any suggestions? Thanks.<br /><br />Kris
<br /><br />What is VZV genome? How big is it?<br /><br />If it is small, just use a text editor to search for the 5 base sequence, u are looking at an exact match anyway.<br /><br />The best way to do it is to write a perl program. Just 5-6 line of code should do it.<br />Hi!
For such searches I'm using the Biology Workbench platform (http://workbench.sdsc.edu) and it has a program called ALIGN. After signing up the workbench, you can just copy the whole sequence (125 kb) and your target (5 b) as two entries and align them by setting the "end-gap weighting" parameter off. If it doesn't work, you can also reverse complement one of the sequences and try again.
-jahan-
QUOTE (kmwpup @ May 9 2007, 03:32 PM)
What I eventually did was search for a 7bp sequence in a blast, just using every combination of the 4 bases to comprise the in the 2 bases tagged on the the 5bp sequence I was interested in.
That's very clever!
-cyberpostdoc-