How to do clustering of proteins on the basis of BLASTall result for all the proteins in any genome?

22 October 2012 1 7K Report

I have done blastall for my all proteins with each other. Now I am stuck in clustering for these all proteins. How to go on in this regard?

Gabriel Rech

You can use MCL (Markov Cluster Algorithm) . You can read "Clustering similarity graphs encoded in BLAST results" in the protocols section. (http://micans.org/mcl/)

Badges
Science topic

More Gaurav Sharma's questions See All

Do anyone here can help us in the field of molecular docking?

We have synthesized various metal complexes with different environment around the metals. Now to see the application of synthesized complexes we need this study also. we are also interested in...

01 March 2021 1,899 2 View

Why does intensity drops as concentration increases?

Is there any reason for decrease in fluorescence emission intensity of HSA,BSA when increase the concentration ?

28 February 2021 3,653 4 View

How does SEA software normally number subsystems?

Dear colleagues, What is the common subsystem numbering system in SEA modelling software (i.e. VA One, AutoSEA2)? Cheers, Feng

27 February 2021 7,073 3 View

Modeling viscosity using model of Chung?

Hello, As part of simulation of gases mixture and water, I need to calculate viscosity of the fluid components and I am using relationships proposed by Chung et al. (1988). The irony is while I...

25 February 2021 8,053 5 View

Genescan gives 3 peaks instead of one?

Hi all, I am doing a genescan analysis for a deleted exon in the patient sample. The amplified region is 215 bp. In the patient sample because of homozygous deletion, no peak is observed while in...

23 February 2021 5,645 1 View

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

How can I retrieve FASTA sequence from gene ID or UID of a Gene ? I have GeneBank IDs ?

I treid to use Entrez Batch, but it redirects me to NCBI site. Is there any script of Linux or Python through which I can download Fasta sequence of list of gene ID ?

21 February 2021 7,783 12 View

How can we study the adsorption efficiency of microgel at the oil-water interface?

I am studing the mircogel at oil-water interface. I want to know the adsorb amount of microgel at the oil water interface. How we can determine this amount?. I will highly appreciate your...

19 February 2021 2,787 1 View

Not able to charge-discharge Li-ion coin cell at higher C rate ?

I am working on cathode material. I have made different Li-ion coin cell against Li metal using commercial available cathode materials such as LCO,LMO, LFP and NMC and also with the lab...

18 February 2021 1,450 3 View

Why at farmer level Cow/Buffalo are not done artificial insemination just after 2 month for yearly calving?

Physiologically in cow, oestrous heat again goes on the peak after 2 months but locally this is not observed and AI is after two months but done after at least 6 months.

17 February 2021 685 4 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

Resistor definition in Piezoelectric bimorph with ANSYS workbench

Hello, good day! I am trying to simulate similar bimorph piezoelectric harvester with below commands. However, the output power doesn't change with resistor value. Please help to find the reason. ET,10,CIRCU94,0 !SET UP RESISTOR R,1,100000 !RESISTANCE VALUE TYPE,10 !SET ELEMENT TYPE E,1,2 !CREATE RESISTOR BETWEEN NODES 1 AND 2 Thanks in advance Regards,

02 March 2021 0 0 View

Why are the velocities so high in my Boussinesq approximation Fluent simulation?

Hello, I have a mechanism where air rises due to convective flows. In this simulation, nothing is driving the air except this. I understand that the Boussinesq approximation only works for small...

02 March 2021 4,910 3 View

What is the characteristic length to determine the Reynolds number for the scattered turbulent fluid flow?

Dear all, I just saw this example in FB on the difference between laminar flow and turbulent flow. The flow from a pipe hits the sink and scattered. The flow from the pipe is characterized as...

02 March 2021 1,999 5 View

How Can I bring as much common elements in steel as possible to calculate stable phase(s) in OpenCalphad?

As I was tweaking step-by-step OpenCalphad6 Macros step1.ocm involving phase and thermal property calculation of a High-speed steel, I could not incorporate more than 6 elements in the steel...

01 March 2021 8,840 1 View