Andrew Perry's Library tagged web_based →  View Popular

"Protein finder is a gendetector. The program finds genes by performing blastx searches of the input sequence against NR. For each high scoring pair the coverage is calculated. The user can set a threshold for the coverage. Every high scoring pair that meets or exceeds this threshold is reported in an embl file. This embl file can be loaded into artemis together with the DNA sequence."

nbc11.biologie.uni-kl.de/...menu - Preview

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.. yet another protein structural alignment tool added to my list ...

topmatch.services.came.sbg.ac.at - Preview

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www.dmbr.ugent.be/...index.php - Preview

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toolserver.org/...index.cgi - Preview

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builder.yaml.de - Preview

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www.positioniseverything.net/...pagemaker_form.php - Preview

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An annotation meta-server. "Annie was born out of the necessity of the Sequence Analysis group to make functional predictions on a wide range of targets arising from in-house projects as well as collaborations. The availability of hundreds of prediction tools makes the effort of functional characterization a tedious tasks with hours spent on sieving through a bewildering range of result formats and outputs."

annie.bii.a-star.edu.sg/...index.jsp - Preview

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swissmodel.expasy.org/...index.cgi - Preview

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a web frontend to many bioinformatics & structural bioinformatics tools, including Modeller (if you have a license key).

mobyle.rpbs.univ-paris-diderot.fr/...portal.py - Preview

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"The AD-ENM (Analysis of Dynamics of Elastic Network Model) server performs analysis of macromolecular dynamics based on a highly simplified physical model --- Elastic Network Model (ENM)"

enm.lobos.nih.gov/index.html - Preview

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Designed for filtering large numbers of protein models based on various properties (solvent accessibility, contact order, RDF shape, secondary structure, etc)

sift.cchmc.org - Preview

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Web-based pipeline for comparative modelling: Template selection->alignment->model building->refinement->evalutation

luna.bioc.columbia.edu/...pipe_int.cgi - Preview

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manaslu.aecom.yu.edu/loopred - Preview

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www.screentoaster.com - Preview

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Plone4bio provides a web-based integrated environment for managing and analyzing biological sequence data. Includes a feature viewer. Backed by BioSQL and Plone.

www.plone4bio.org/trac - Preview

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Creates attractive 'bubble' domain diagrams based on a simple text based definition provided by the user. Provides stable URLs of the images (via encoding the diagram description in the GET query parameters) - like Google Charts for protein domain architecture diagrams :)

au.expasy.org/...mydomains - Preview

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enoLOGOS is a web-based tool that generates weighted sequence logos directly from energy measurements or other sources, including energy measurements, probability matrices, alignment matrices, count matrices and aligned sequences. Furthermore, enoLOGOS can represent the mutual information of different positions of the consensus sequence.

biodev.hgen.pitt.edu/...enologos.cgi - Preview

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partifold.csail.mit.edu - Preview

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The Profile Comparer (PRC, Martin Madera) is a program for aligning and scoring profile hidden Markov models.

www.ibi.vu.nl/prcwww - Preview

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Via profile-profile alignment. Alignments to PDB sequences can be easily fed into a web-based version of SCWRL and Jackal for generating homology models.

ffas.ljcrf.edu/...ffas.pl - Preview

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