search for: nucleic

Displaying 14 results from an estimated 14 matches for "nucleic".

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2018 May 03
3
Package for Molecular Properties
...a nucleotide sequence 1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law) 2. calculate molecular weight 3. return it's complementary sequence I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids. Any pointers, etc. would be great. thank you in advance Indr
2010 Jan 03
2
bio3d package not installing
Is it just me, or is the bio3d package no longer available? Is there another way to do a reasonable nucleic acid sequence alignment in R? Thanks, Jonathan [[alternative HTML version deleted]]
2018 May 03
0
Package for Molecular Properties
...; > 1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law) > 2. calculate molecular weight > 3. return it's complementary sequence > > I was able to find several packages that can do similar calculations for an amino acid sequence for proteins but none for nucleic acids. > > Any pointers, etc. would be great. > > thank you in advance > Indr > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the p...
2006 Nov 16
2
question about capscale (vegan)
...ilarity matrix and I am intended to use it as 'distance' argument. But then, I don't know what kind of data must be in 'comm' argument. I don't understand what type of data must be referred as 'species scores' and 'community data frame' since my data refer to nucleic distances between different sequences. I would be very grateful if you could help me with this fact in any manner. Thank you in advance for your help. Regards, Alicia
2017 Aug 31
0
The aphid package for analysis with profile hidden Markov models
Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export, tree-based sequence weighting, simulation, and implementation of the forward, backward and Viterbi algorithms for calculating...
2007 Aug 18
1
doubt about string comparison
...names in both of them. My arrays are for example Array1 Array2 GAP4 HIST1B-histamine.... MFG12 SNRPD-signal induced... CFH1A RNF-ribose nucleic... My array 2 ,has description of the abbreviation ,how can I remove the description part before using intersect command to match common names in array1 and array2. the description and abbreviation are separated by a hyphen --. I tried using matlab ,but due to the large file size it didnot work....
2017 Aug 31
0
The aphid package for analysis with profile hidden Markov models
Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export, tree-based sequence weighting, simulation, and implementation of the forward, backward and Viterbi algorithms for calculating...
2018 May 03
1
Package for Molecular Properties
...xtinction coefficient at 260 nm for (Beer-Lambert's law) >> 2. calculate molecular weight >> 3. return it's complementary sequence >> >> I was able to find several packages that can do similar calculations for >> an amino acid sequence for proteins but none for nucleic acids. >> >> Any pointers, etc. would be great. >> >> thank you in advance >> Indr >> >> ______________________________________________ >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listi...
2010 May 11
1
comparing and combing files
...uction,Sensory perception Cell surface receptor mediated signal transduction,Pheromone response A_51_P100227 NM_023579.4 HEAT,Importin-betas N-terminal,Armadillo-like helical IMPORTIN BETA-3,IMPORTIN BETA Intracellular protein traffic,Biological process unclassified,Nucleoside, nucleotide and nucleic acid metabolism,Transport Nuclear transport,RNA localization A_51_P100227 NM_023579.4 HEAT,Importin-betas N-terminal,Armadillo-like helical IMPORTIN BETA-3,IMPORTIN BETA Intracellular protein traffic,Biological process unclassified,Nucleoside, nucleotide and nucleic acid metabolism,Transport...
2004 Nov 16
1
gcrma package
Hi ! I would like to understand where do affinity.spline.coefs used in function compute.affinities come from ? library(gcrma) data(affinity.spline.coefs) affinity.spline.coefs X1 X2 X3 X4 X5 X1 -0.55004171 -0.58579091 -0.08870557 -0.47774242 0.23205570 0.58002746 X2 X3 X4 X5 X1 X2
2006 Jul 25
0
seqinr updated : release 1.0-5
...mpute the molecular weight of a protein is now available. http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/pmw.html o A new function reverse.align() contributed by Anamaria Necsulea is now available to align CDS at the protein level and then reverse translate this at the nucleic acid level from a clustalw output. This can be done on the fly if clustalw is available on your platform. http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/reverse.align.html o An undocumented behavior was reported by Guy Perriere for uco() when computing RSCU on sequences w...
2006 Jul 25
0
seqinr updated : release 1.0-5
...mpute the molecular weight of a protein is now available. http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/pmw.html o A new function reverse.align() contributed by Anamaria Necsulea is now available to align CDS at the protein level and then reverse translate this at the nucleic acid level from a clustalw output. This can be done on the fly if clustalw is available on your platform. http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/reverse.align.html o An undocumented behavior was reported by Guy Perriere for uco() when computing RSCU on sequences w...
2001 May 30
2
new book
Just thought I would mention that there is a new O'Reilly book out, "Developing Bioinformatics Computer Skills", which is ok, pretty superficial about some things but at least it lets you know what is happening and where. R gets a few pages in there, 394-396, mostly nice press and accurate except that Bill Venables (hi Bill) may be surprised to find out that he is a member of the
2006 Jun 18
2
analyze amino acid sequence (composition)of proteins
Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some