Bioinformatics and Computational Biology

• Dushyant Singh

  I want to do a project for 1year, in bioinformatics, can anyone help me on which topic i shuld work onto.. i m persuing MTech..

  Its my major project....
• Ravi Kanth

  Suggestions of a server or a package to produce hydropathy plots?

  As i am comparing many proteins sequences, I have chosen hydropathy plots as a criteria to compare hydrophobic to hydrophilic amino acids in each protein. Should it be possible to by the software toAs i am comparing many proteins sequences, I have chosen hydropathy plots as a criteria to compare hydrophobic to hydrophilic amino acids in each protein. Should it be possible to by the software to over lap all the sequences in to one plot?

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  • 
    Ravi Kanth replied

    Thanks alot, Stefania, I have chosen to use expasy tool (http://web.expasy.org/protscale/), I am having few glitches, as I would want to use hydropathy plots as a mode of comparison of 7 differentThanks alot, Stefania, I have chosen to use expasy tool (http://web.expasy.org/protscale/), I am having few glitches, as I would want to use hydropathy plots as a mode of comparison of 7 different proteins sequence composition, which i plan to do so by overlapping the plots of 7 proteins in different colors, I did try it in expasy, but i am able to get one plot at a time. So is it possible for me to upload 7 different sequences at once to get 7 plots in the same graph. Kindly advice.

    1 day ago
• Zhenyu Wang

  Molecular Classification of Cancer, not enough samples?

  To develop a molecular classifier for cancer diagnostic, we need numbers of samples to train the classifier, many researchers stated that: the sample size is still very small (within 200). forTo develop a molecular classifier for cancer diagnostic, we need numbers of samples to train the classifier, many researchers stated that: the sample size is still very small (within 200). for example, in http://www.broadinstitute.org/mpr/publications/projects/Leukemia/Golub_et_al_1999.pdf , the sample size is smaller than 100. Questions: are there more samples available now? Or there are still limited samples can be used for training classifiers (due to the issues like cross-lab evaluation)?

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    Mario Guarracino replied

    The launch data portal of the cancer genome atlas may be a good starting point: http://cancergenome.nih.gov/

    2 days ago
• Shawon Barua

  Torsian Angle

  Is the torsian and dihedral angle the same? How can I measure torsian angle of amino acid residues of a protein sequence?

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    Christian Schudoma replied

    Try DANGLE (http://kinemage.biochem.duke.edu/software/dangle.php) for computing the phi/psi - torsions in a protein structure.

    3 days ago
• Gorka Lasso

  How to detect paralogs in a list of protein pairs in a high-throughput manner

  I have a long list of pair of proteins, described by their uniprot code, in which to identify those pairs corresponding to paralogs. For this, and based on Perez-Bercoff et al. (see link), I plan toI have a long list of pair of proteins, described by their uniprot code, in which to identify those pairs corresponding to paralogs. For this, and based on Perez-Bercoff et al. (see link), I plan to run a pairwise alignment of each pair of proteins (using BLAST) and extract the corresponding evalue and the percentage of aligned residues. Proteins will be considered paralogs only if the e-value of the pairwise alignment is =< 1e-20 and at least 50% of the residues are aligned. Any feedback on this approach and alternative (or complimentary) strategies is more than welcome.

  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2894830/?tool=pubmed

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  • 
    Max Robinson replied

    Thomas, agreed. Note that I said BLAST was _intended_ to identify homologs. You are of course correct that BLAST does that by detecting similarity; what kind of similarity it detects is defined byThomas, agreed. Note that I said BLAST was _intended_ to identify homologs. You are of course correct that BLAST does that by detecting similarity; what kind of similarity it detects is defined by the scoring matrix, which is not part of BLAST itself. The matrices most commonly used with BLAST are intended to detect similarity due to homology, and appears to be the kind of matrix that would be most useful for Gorka's question. A BLAST score--not an E-value, the integer score from which the E-value is derived--ultimately represents a log-likelihood ratio between two hypotheses: (A) the sequences are similar due to descent from a common ancestor, versus (B) the sequences are similar by chance. A high score only means that model (A) fits the data far better than model (B); this could happen because (1) model (A) in fact fits the data very well, or (2) model (B) fits the data very poorly, or (3) some mixture of the two. As an example of (2), take transcriptional activation domains. These domains, due to their function, have an unusual set of amino acid frequencies. Thus, a pair of transcriptional activation domains will have the same unusual distribution of amino acid frequencies, and will show more similarity _by chance_ than predicted by model (B), resulting in a higher score than model (B) would predict. No automated analysis tool, whether BLAST or InParanoid, should be used without a critical evaluation of the results it produces.

    3 days ago
• Priyanka Patel

  Modelling of sequenced gene product

  I have sequenced an important part of a variant of the DHPS gene containing 500bp encoding the important domain part of protein, but not the full gene, by Applied Biosystem 16 capillary. Now I wantI have sequenced an important part of a variant of the DHPS gene containing 500bp encoding the important domain part of protein, but not the full gene, by Applied Biosystem 16 capillary. Now I want to obtain the structure of the full protein contained in my sequenced domain. Can I use bioinformatics modelling approaches to model the full protein? I have the template structure of this protein as wild type.

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    Rick Anthony Ricketson replied

    Modeller is great when you're with an unknown. Once you have the template and new extended model, bring the template into Chimera and superimpose your model using the sequence>Match>align tool. YourModeller is great when you're with an unknown. Once you have the template and new extended model, bring the template into Chimera and superimpose your model using the sequence>Match>align tool. Your model is already threaded so that's not an issue. Once superimposed, delete the template. Done except for the colors.

    3 days ago
• Omprakash Tanwar

  Can I develop homology model for DPP-8 and DPP-9 proteins?

  Can I develop homology model for DPP-8 and DPP-9 proteins? their ID are >gi|11095187 and >gi|90082057. Actually they are nucleotide sequences. I am working on development of novel DPP-4 inhibitorsCan I develop homology model for DPP-8 and DPP-9 proteins? their ID are >gi|11095187 and >gi|90082057. Actually they are nucleotide sequences. I am working on development of novel DPP-4 inhibitors and want to develop the homology model for DPP-8 and DPP-9 proteins. They are homologous to DPP-4 and there are number of crustal structures available for DPP-4 but non for DPP-8 and 9. The ligands should be selective towards DPP-4 other wise they show toxicity. My aim to develop the homology model for DPP-8 and 9 and use it for predicting the selectivity of DPP-IV ligands as assay kit for DPP-8 and 9 are too costly. Any advice? Thanks

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    Omprakash Tanwar replied

    Thank you dear all for help and guidance

    4 days ago
• Dody Gh

  Can anyone tell me how to register a new mutation in the gene bank?

  I'm doing gene sequencing in metabolic disorders and I hope to tell me the steps that should I follow if I discovered a new gene mutation to register this in the gene bank?

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    Raymond Dalgleish replied

    You ought to also find out if there is a locus specific database (LSDB) for the gene in which you have found the mutation and submit it directly to the LSDB. Submission of mutations to dbSNP is aYou ought to also find out if there is a locus specific database (LSDB) for the gene in which you have found the mutation and submit it directly to the LSDB. Submission of mutations to dbSNP is a good first step, but there is no automatic forwarding of data to the relevant LSDB. You can find a comprehensive list of LSDBs at: http://www.gen2phen.org/data/lsdbs

    5 days ago
• Sneha Paul

  Any references and links for phytochemicals?

  I am working on phytochemicals and would like to know more links or websites that give more information about pytochemicals and from where these compounds can be downloaded.
• Neha Sanghi

  Can anyone tell me the software for doing differential expression analysis of RNA-seq data?

  I want to do the differential expression analysis of RNA-seq data. My sample does not contain biological replicates. I tried using partek, but it does not calculate differential expression at geneI want to do the differential expression analysis of RNA-seq data. My sample does not contain biological replicates. I tried using partek, but it does not calculate differential expression at gene level without biological replicates.

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    Lionel Moulin replied

    About CLC Genomics, i use it also for mapping and RNA seq analysis. Unfortunately you can only work with PRKM and not assess stiatistical variance across replicates, an approach that you have inAbout CLC Genomics, i use it also for mapping and RNA seq analysis. Unfortunately you can only work with PRKM and not assess stiatistical variance across replicates, an approach that you have in DESeq and EdgeR that gives you a better assessment of data variation. Another thing i point out in CLC, the mapping excludes a lot of sequences (25%) due to a "too high" segregation of errors, while unix softwares as ssaha2 that uses k-mer approaches seems to integer more sequences so you end up with better statistics. But I might have not look too deep into CLC to modify mapping parameters. About EdgeR, did somebody compared DESeq and EdgeR and can give a feedback on results using the 2 methods? Cheers, Lionel

    5 days ago
• Nutan Chauhan

  Showing secondry structural elements with the aligned amino acid sequence

  Can anybody help me in using ESPript (http://espript.ibcp.fr/ESPript/ESPript/). I want to show the secondary structural elements with the aligned sequence. When I upload alignment file inCan anybody help me in using ESPript (http://espript.ibcp.fr/ESPript/ESPript/). I want to show the secondary structural elements with the aligned sequence. When I upload alignment file in multalign/clustalW format I get aligned sequence in pdf/post script format but whenever I tried to upload DSSP/PDB format along with the aligned file I only get "fatal error".

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    Nutan Chauhan replied

    Dear Ranjan, thanks a lot for your help. Thank you very much

    5 days ago
• Nutan Chauhan

  Protein structure prediction

  My aim is to find a better lead compound by in silico approach. The crystal structure of the protein which I am working upon is not yet available, so I performed Blastp against PDB but no goodMy aim is to find a better lead compound by in silico approach. The crystal structure of the protein which I am working upon is not yet available, so I performed Blastp against PDB but no good template (very very bad quality, can not be used for homology modeling purpose) was found. I submitted this protein to i-tasser server and it gave me a model with 87% allowable and 1.3% disallowable regions for amino acids in ramachandran plot. My queries are: 1. As the source of my protein is a protozoa and my main goal is to find better lead compounds, can I use a human protein sequence as template to model my protein (i-tasser exclusively used human sequences)? Will there be any problem if I use this modeled protein (generated from human protein structure) for further docking purposes? If yes, why? 2. Can the quality of this model be improved by MD simulation? To what extent?

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  • 
    Harinder Singh replied

    Try using HHPred , it might give you good template.

    6 days ago
• Talita Colombo

  Could someone advise on which software I should use to find the catalytic site of the protein?

  I need to find the catalytic site of the GSK protein, in order to analyze for proximities.

  Recent replies ⋅ Show All (66)

  • 
    Zahida Parveen replied

    yup METAPOCKET 2.0 online tool ( http://projects.biotec.tu-dresden.de/metapocket/) is very good one

    6 days ago
• Ali Ramazani

  Does anyone know how to calculate the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of lead compounds?