User: Erik Wright
Erik Wright • 210
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Posts by Erik Wright
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... Thanks Valerie,
Your explanation was much better than the one I found in the
?pairwiseAlignment man page. It states:
"global" = align whole strings with end gap penalties ... "global-
local" = align whole strings in pattern with consecutive subsequence
of subject
Obviously the "whole strings" wer ...
written 7.8 years ago by
Erik Wright • 210
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... Hello,
I have been using the Biostrings function "pairwiseAlignment" lately
to perform sequence alignments. I have discovered that with difficult
alignments it sometimes returns incomplete patterns. For example:
pairwiseAlignment("ACTGACTGACTGACTG","AAGAAGAGTTATGGGAGTAACTGACC")
Global PairwiseAl ...
written 7.8 years ago by
Erik Wright • 210
• updated
7.8 years ago by
Valerie Obenchain • 6.7k
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... Hi Benilton,
Yes, all I need to do was upgrade R. Apparently the CRAN mirror I was
using no longer exists, so apt-get updates were not occurring
automatically and I never noticed.
Thanks,
Erik
On Aug 21, 2010, at 9:05 PM, Benilton Carvalho wrote:
> You should start by upgrading R.
>
> ...
written 9.3 years ago by
Erik Wright • 210
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... Hello,
I am attempting to upgrade the Biostrings package on a linux box
running Ubuntu (10.04).
If I use:
> source("http://bioconductor.org/biocLite.R")
> biocLite("Biostrings")
Afterwards the computer still has the same (presumably outdated)
version (2.14.12).
So I tried installing the dev ...
written 9.3 years ago by
Erik Wright • 210
• updated
9.3 years ago by
Benilton Carvalho • 4.3k
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... Hi Patrick,
Thanks, this looks promising. Three possible complications are:
(1) The fragments are not all the same width. Is this possible with
Pdict?
(2) I allow a variable number of mismatches based on each individual
fragment's width.
(3) The fragments sometimes include ambiguity letters (I ...
written 9.4 years ago by
Erik Wright • 210
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... Hello,
Lately I have been working on counting sequence fragments in larger
sets of sequences. I am searching for thousands of fragments of 30 to
130 bases in hundreds of thousands of sequences between 1200 and 1600
bases. Currently I am using the following method to count the number
of "hits":
# ...
written 9.4 years ago by
Erik Wright • 210
• updated
9.4 years ago by
Patrick Aboyoun ♦ 1.6k
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... Hello,
What limits the number of sequences and size of sequences that are
part of a DNAStringSet? Are there any way to change these limits?
On my home laptop I can create a DNAStringSet of about sixty thousand
sequences of length 1500. On my desktop I can only make a
DNAStringSet of twenty thous ...
written 9.5 years ago by
Erik Wright • 210
• updated
9.5 years ago by
Steve Lianoglou ♦ 12k
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Comment:
C: Alignment viewer?
... Very good idea! Thanks Thomas!
On May 4, 2010, at 4:30 PM, Thomas Girke wrote:
> If it helps, here are a few examples for handling multiple/pairwise
> alignments in Biostring's XStringSet container class and viewing
them as
> html files in a browser (StringSet2html):
> http://manuals ...
written 9.6 years ago by
Erik Wright • 210
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... Hi all,
Does anyone know of a package that I can use to view alignments in R?
Basically I want to display a long DNAStringSet sequence by sequence:
Seq1: ACTAGGAGCTYA...
Seq2: ACTACGAGCTCA...
Seq3: ACTAGGACCTNA...
etc....
I just wanted to check if there is one already available so that I
don't ...
written 9.6 years ago by
Erik Wright • 210
• updated
9.6 years ago by
Thomas Girke • 1.7k
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Comment:
C: consensusString Function
... Hi Patrick,
Thanks for closing the loop on this issue. I have a question about
the outputs you show below:
If two strings are ACAG and ACAR where R can be A or G, then it makes
sense to me that the consensus is ACAR.
Why then is an N treated differently than an R? If two strings are
NNNN and AC ...
written 9.7 years ago by
Erik Wright • 210
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