Bioinformatics and Computational Biology

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Question:
New Good alignment visualization software with command line interaction?
I want analize a series of alignments, while aligning from the command line with clustal omega. I'm analyzing the alignments with clustalX, but it's s... [more]

I want analize a series of alignments, while aligning from the command line with clustal omega. I'm analyzing the alignments with clustalX, but it's somewhat difficult since the sequences with which I'm working are large (11kb+), and I want to view the alignments with less zoom. So I would like to know a good program to view those alignments that can be called from the command line, any suggestions?

By Carlos Bueno · Universidad Peruana Cayetano Heredia

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3 Best free tool to identify the active site of the protein
By Sunil Kumar Sahu · Annamalai University

Shubhankar Bhattacharyya · Defence Research and Development Organisation

i will prefer Q-site finder....from this site u can download of ur pocket information http://www.modelling.leeds.ac.uk/qsitefinder/

i will prefer Q-site finder....from this site u can download of ur pocket information http://www.modelling.leeds.ac.uk/qsitefinder/

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14 Is it possible to build a reliable model of a protein ternary complex from sequence data?
By Uttam Pal · Indian Institute of Chemical Biology

Boguslaw Stec

Dear Uttam, It was really informative to read this entire discussion, especially changing positions of some of the people with learning new details. A... [more]

Dear Uttam, It was really informative to read this entire discussion, especially changing positions of some of the people with learning new details. As with every science problem it turns out that with some modifications something is doable after you hack at it, and hack at it. My only 2 cents here is that over the years people developed methods for the exact task as you are facing that were not mentioned here. 1) There are several databases on the web that describe the protein-protein interactions on many different levels including details (Biogrid, String, Mips, Pips etc.) 2) There are sophisticated protein-protein docking methods, some of them quite successful (Rossetta, Zhang) 3) There methods that allow you to map the most likely interacting surfaces by looking at remote homologies and co-evolution (i.e. Lichtarge, from Baylor) 4) There are methods for using any experimental constraints and building the complex (Sali, San Francisco, Gerstein, Yale) 5) You can use some of the newest ontology derived methods of association that use the web info normally not integrated by other sources. But, I generally agree this is a very difficult problem. Modeling even a single component would be a challenge. My experience with membrane or peripheral membrane proteins is that they undergo significant conformational changes upon binding, so you would be stepping into a substantialy new territory by predicting one of the active conformations of these components, selecting it and using it productively. This would be like executing the decision tree before you know how it looks like. How would you decide which of the models (if you get several models for contributing factors) to use in quaternary assembly? Proteins are not stiff, they are mobile and malleable. Good Luck.

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3 What work has been done to determine the degree to which any single strand of DNA exhibits complementary subsequences?
By William Buckley · California Evolution Institute

Vincenzo Bonnici · Università degli studi di Verona

May be you can use two suffix array, one for the upstream and one for the downstream, and compare them.

May be you can use two suffix array, one for the upstream and one for the downstream, and compare them.

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4 difference between HLA Allele frequency and HLA phenotype frequency
By Stanley Meribe · Kumamoto University

Stanley Meribe · Kumamoto University

Ok, I got the drift now. Thanks

Ok, I got the drift now. Thanks

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2 Which website is best one for downloading dataset in medical domain?
By Purusothaman Gnanapandithan · Rathnavel Subramaniam College of Arts and Science

Nitish Mishra · The Samuel Roberts Noble Foundation

It's depends upon your study.. DrugBank (http://www.drugbank.ca) is a very good database for drug molecules and targets. KiBank, PubChem, ChemStar, Z... [more]

It's depends upon your study.. DrugBank (http://www.drugbank.ca) is a very good database for drug molecules and targets. KiBank, PubChem, ChemStar, ZINC etc are very good database. You must visit http://www.click2drug.org, it will provide you lots of information. Hope it can help you.

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8 Software to identify the introns and exons present in a sequence
By Raksha Bawankar · Vellore Institute of Technology

Ekaterina Shelest · Hans-Knöll-Institut

For the gene prediction the best tool is Augustus(http://bioinf.uni-greifswald.de/augustus/submission). If your species is already in the list (so th... [more]

For the gene prediction the best tool is Augustus(http://bioinf.uni-greifswald.de/augustus/submission). If your species is already in the list (so the tool is trained for it), you have only to submit the sequence and press te button. If the tool is not yet trained for your species, select any closely related species, better take 2 or 3 of them. In mot cases thisgives more or less reliable results.

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2 I want to know what is +1 value and -1 values for response surface methodolgy software?
By Margi Shelat · Kadi Sarvi Vishwavidyalaya University

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8 -how to use g_energy command
By Ayzeha Kalsoom · University of Karachi

Bhavaniprasad Vipperla · Vellore Institute of Technology

I do agree with Felix, when u give the extension -deffnm it would give different outputs, .edr file being one of them. I would recommend you to go thr... [more]

I do agree with Felix, when u give the extension -deffnm it would give different outputs, .edr file being one of them. I would recommend you to go through the gromacs tutorials and get to know about the output options for better understanding. Goodluck

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96 Which is the best online tool (free) for designing gene specific primers?
By Samiksha Prasad · University of Florida

Shirin Mirlohi · Shahrekord University

Hi, I normally use primer3 for primer design and NCBI primer BLAST for double checking :) Good luck

Hi, I normally use primer3 for primer design and NCBI primer BLAST for double checking :) Good luck

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1 Does SAMTools considers replaced nucleotides for N while calling the variants?
By Sourav Nayak · Jawaharlal Nehru Centre for Advanced Scientific Research

Paul Costea · European Molecular Biology Laboratory

bwa will replace N's in the reference with a random nucleotide. However, N's in the read remain N's. SAMTools will use the original reference so the b... [more]

bwa will replace N's in the reference with a random nucleotide. However, N's in the read remain N's. SAMTools will use the original reference so the bwa indexing scheme won't matter. Thus, this little bwa trick will in no way influence your variant calling.

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1 Protein-Protein Docking and Drugs
By Devashish Das · Aarupadai Veedu Institute of Technology

Arvind Kumar · Sri Sathya Sai Institute of Higher Learning

I think you can look at Hex protein-protein docking.................. GRAMM-X Protein-Protein Docking Web Server vakser.bioinformatics.ku.edu/resource... [more]

I think you can look at Hex protein-protein docking.................. GRAMM-X Protein-Protein Docking Web Server vakser.bioinformatics.ku.edu/resources/gramm/grammx/

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1 Can anyone help to find more structure properties of bio sequence?
By Nooruldeen Qadir · University of Sulaimani

Arvind Kumar · Sri Sathya Sai Institute of Higher Learning

I think structural annotation is available for all proteins at SCOP and CATH protein classification database..... Meanwhile if it analysis of protein ... [more]

I think structural annotation is available for all proteins at SCOP and CATH protein classification database..... Meanwhile if it analysis of protein at various level of structural organisation you can have a look at array of tools available at http://www.expasy.org/tools/

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20 Is there any good protein protein interaction prediction software or tools?
By Rethinamalliga Gunasekaran · Alagappa University

Utpol Das · South Asian University

you can also try this: http://dip.doe-mbi.ucla.edu/dip/Main.cgi

you can also try this: http://dip.doe-mbi.ucla.edu/dip/Main.cgi

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4 Can anyone please suggest me a pattern recognition software to identify the 3'UTR regions?
By Amruta Mhashilkar · University of South Florida

Shirin Mirlohi · Shahrekord University

I've used Dr. Cohen's method before and it works perfectly :) good luck

I've used Dr. Cohen's method before and it works perfectly :) good luck

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Question:
New What are the approaches or softwares i should use to determine which carbohydrate molecules have enzymatic activities?
By computation how to find out the carbohydrate molecules which have catalytic activity?

By computation how to find out the carbohydrate molecules which have catalytic activity?

By Nayem Zobayer · Shahjalal University of Science and Technology

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7 What are the unsolved problems in systems biology?
By Aurélien Mazurie · Montana State University

Giovanni Colonna · Second University of Naples

one of the main goals of systems biology is to quantitatively model the molecular mechanisms of biological phenomena by integrating data at different ... [more]

one of the main goals of systems biology is to quantitatively model the molecular mechanisms of biological phenomena by integrating data at different levels (genomics, transcriptomics, proteomics, metabolomics, and so on). If only pursue this goal you have all of biology available. However, the systems biology is also highly multidisciplinar thus you need also an appropriate team of researchers. This is all.

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1 Does anybody have whole sequence information of pART7 vector?
By Hana Zandkarimi · University of Tehran

Sadeeq ur Rahman · VU University Amsterdam

http://nanolight.com/Uploads/121%20%20pART27%20info%20PDF.pdf. this is the general map that would help you out for cloning but if you need the whole s... [more]

http://nanolight.com/Uploads/121%20%20pART27%20info%20PDF.pdf. this is the general map that would help you out for cloning but if you need the whole sequence you need to ask it from the provider

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176 Statistical signiﬁcance vs. Biological relevance
By Zhenyu Wang · University of Oxford

Joanna Cross · Deutsches Institut für Lebensmitteltechnik

Hi! This is actually a case by case answer as a biologist will look for changes in appearance and productivity. Take the example of a mutant plant tha... [more]

Hi! This is actually a case by case answer as a biologist will look for changes in appearance and productivity. Take the example of a mutant plant that is statistically 20% shorter. The decrease in biomass production is noticeable. On the other hand, if a mutant has an enzyme 30% less active than that of wild type, the difference can be very easily compensated by regulatory changes. Hence, the mutant may behave exactly like a wild type. This is one of the reasons why we typically consider a twofold threshold for gene expression changes even if smaller variations are statistically significant.

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7 When does PolII occupancy at regulatory regions change independently of chromatin state?
By Daniel Cohen · University of Pennsylvania

Francisco Navarro · Universidad de Jaén

Concerning pol II occupancy, does anyone know what happens, in S. cerevisiae, in a shift from 30-37 ºC for 30 min, in genes like PMA1, PYK1, etc? (I ... [more]

Concerning pol II occupancy, does anyone know what happens, in S. cerevisiae, in a shift from 30-37 ºC for 30 min, in genes like PMA1, PYK1, etc? (I know Pol II occupancy increases in HSP genes and decreases in RP genes).

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28 Suitable agent based modeling framework for learning ABM in biology?
By Samuel Lampa · Uppsala University

Martina Husakova · University of Hradec Králové

You are welcome :-).

You are welcome :-).

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Question:
New What is the way to predict the transcription factor (TF) activity in a diseased state using insilico methods
For Transcription factor, it is not just expression level but activity that matters. So how using in silico methods one can establish that that the TF... [more]

For Transcription factor, it is not just expression level but activity that matters. So how using in silico methods one can establish that that the TFs are active in the disease condition.

By Subhash Agarwal · Institute of Cytology and Preventive Oncology

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25 Protein Sequence Alignment
By Shawn Lu · Massachusetts Institute of Technology

Fatima Gaboun · Institut National de Recherche Agronomique de Rabat

Like Julian, using SUPERFAMILY database,.the appraoch give the good result

Like Julian, using SUPERFAMILY database,.the appraoch give the good result

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3 How to ubiquitinate the protein by in silico approaches?
By Muhammad Ayaz Anwar · Ajou University

Muhammad Ayaz Anwar · Ajou University

Thank you Uttam Pal and R. Namdeo for such a prompt reply. I will go for Schrodinger Maestro as this suits better to my situation

Thank you Uttam Pal and R. Namdeo for such a prompt reply. I will go for Schrodinger Maestro as this suits better to my situation

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5 Need help for psipred tool...
By Arif Tanmoy · University of Dhaka

Osmar Norberto de Souza · Pontifícia Universidade Católica do Rio Grande do Sul

Arif, Try this: Do a BLAST search to annotate the sequences. A simple BLASTp is enough to start, but the search can be refined by using PSI-BLAST and,... [more]

Arif, Try this: Do a BLAST search to annotate the sequences. A simple BLASTp is enough to start, but the search can be refined by using PSI-BLAST and, now, DELTA-BLAST. If the sequences have homologues with known 3D structures in the PDB, they will appear as a result of your search. It is always advisable to learn as much as possible about your sequences before starting automatic server predictions of protein secondary and tertiary structures. Good luck!

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4 I want to install DSSP for secondary structure analysis for GROMACS?
By Budheswar Dehury · Assam Agricultural University

Vikrant Singh · Martin-Luther-Universität Halle-Wittenberg

for installation you can use the installation instruction which is available here : http://www.gromacs.org/Documentation/Installation_Instructions

for installation you can use the installation instruction which is available here : http://www.gromacs.org/Documentation/Installation_Instructions

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