How to score the similarity of DNA sequence to a motif/profile?

04 April 2013 1 3K Report

Any recommended method to measure the similarity?

Profile HMMs are a possibility, see http://bioinformatics.oxfordjournals.org/content/14/9/755.full.pdf or software hmmer.

If your motif/profile does not require deletions or insertions to match, using PSSMs (PWMs) should work, see http://en.wikipedia.org/wiki/Position-specific_scoring_matrix or software MATCH

Badges
Science topic

More Jia-Yu Chen's questions See All

How to simulate enzymatic hydrolyis of sucrose in a CSTR coupled with ultrafiltration membrane with comsol?

Dear all, I am trying to simulate the enzymatic hydrolysis of sucrose with invertase in CSTR in Comsol. The reaction pathway is such that Sucrose + Water -> Fructose + Glucose. It is desired...

27 January 2021 2,525 4 View

How to design an Ultrafiltration membrane for a CSTR?

Dear all, I am designing an Ultrafiltration (UF) membrane coupled with a CSTR. It is desired to utilized a dead end stirred reactor. The main purpose is to separate the enzyme used from the final...

27 January 2021 7,924 1 View

Submission of the Materials Studio jobs to the remote Linux cluster?

I am doing some simulations using the Forcite module in Materials Studio. As the speed of this calculation on my workstation computer is unacceptably slow, I am trying to submit my job to the...

14 January 2021 8,653 1 View

Generate a structure file through PGDSpider?

Hi, I am trying to generate a structure file through PGDSpider, for a diploid organism, where each locus is in two consecutive columns in one row, rather than data for each individual be stored...

29 December 2020 5,169 1 View

Why abnormal thrust force was generated in simulation of CFRP drilling?

I am doing some simulations of drilling carbon fiber reinforced plastics (CFRP) with Abaqus/Explicit. 3D Hashin's damage model with damage evolution has been defined for the CFRP composite. The...

20 November 2020 6,715 1 View

Could anyone recommend a kit to isolate exosome from cell culture supernatant?

Hello, I'm working with immortalized HUVECs low and I'm trying to study their exosomal RNA contents. Could anyone recommend an effective kit to isolate exosomes from cell culture supernatant?...

31 October 2020 4,252 5 View

What's the connection between PERMANOVA and SIMPER?

I have a pair of groups that are not significantly different in PERMANOVA (p > 0.05), yet in SIMPER the average dissimilarity between these two groups are very high, even higher than other...

13 August 2020 8,217 2 View

How should I design the N-terminal VC plasmid of BiFC assay?

I'm going to detect protein-protein interaction with BiFC assays and my target proteins are ER retention with KDEL motif. so I want to fuse VC to the N-terminal of my protein. My question is if...

22 July 2020 3,456 1 View

How to correct OBS horizontal components when the instrument tilted?

I want to rotate the 1,2 components of OBS to the R, T components, but the SAC command running results show that the two components are not horizontal. Could anyone can teach me how to correct...

06 July 2020 2,536 3 View

Hydrogel's pore size at nano scale?

Hi all! I am selecting hydrogel materials for my DNA application. The ideal hydrogel should have a pore size between several to tens of nm and the pore to be negatively charged. The purpose of...

19 February 2020 3,862 3 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

How to calculate average trend in maximum annual NDVI from MODIS?

I am wanting to calculate the average trend in maximum annual NDVI in Iceland from 2010-2020 using MODIS MYD13Q1 V6. How would I do this? I have currently inserted the NDVI bands from the MODIS...

02 March 2021 752 2 View

Why does two different bioinformatics tools for the same proteins show different subcellular localizations?

During a computational analysis, I found that for a protein of a plant, two different subcellular localizations are seen using CELLO and WoLF PSORT. For example, in CELLO, it identified the...

01 March 2021 6,729 2 View

What is the most suitable server for predicting protein structures in bacteria?

I have used the i-Tasser several times, however it has been unavailable for several days. I tried the swiss-model, but the output was not very pleasant due to the model used. Is there any other...

28 February 2021 4,521 3 View

What is the difference between genotype and haplotype data in the ped format?

Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...

27 February 2021 1,965 1 View

I have need of XRD graph analysis software for phase identification. Can you please provide links for software tools which can be downloaded?

i am trying to download x'pert high score software, but can't download it. please do suggest software for phase analysis

24 February 2021 5,687 4 View

Please suggest me the simplest way to understand the in-silico analysis of any gene?

I want to understand the basics of docking, and also know about all bioinformatics tools which are free of coast and helpfull in in-silico analysis?

22 February 2021 8,879 2 View

Is there a Constitutive model for concrete with Sea-Sand?

Hi I am running a simulation in Abaqus for a concrete beam. Its fine aggregate replaced with sea-sand. I was wondering if I could find studies that measured the ultimate strain of concrete made...

22 February 2021 6,409 2 View

How can we measure the reliability and validity of our survey questionnaire?

We are conducting survey research on COVID-19 misinformation among students. How can we validate our survey for it to produce valid and reliable data? Also, what statistical tools can we use to...

16 February 2021 678 3 View

How to remove the species data from rda data frame in R (only remain the sites/samples point)?

Dear everyone, When I using the rda function in r, I met this question. As you can see in the figure, there are a lot of deep blue points which refers to the species. But I would like remain...

15 February 2021 8,982 2 View