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indra.mullins.microbiol.washington.edu

Computational Biology Software — Mullins Lab

Mullins Lab Computational Biology Software. Uses molecular, computational, and virus biology techniques to provide insights into the relationship between HIV and its human hosts in an effort to fight the AIDS pandemic. Below is a catalog of software we’ve produced during this work to help us and others study retroviruses. Applications marked requires login are currently only available to lab members and our collaborators. Please email us. If you’d like to learn more about them. A platform for the collect...

http://indra.mullins.microbiol.washington.edu/

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Computational Biology Software — Mullins Lab | indra.mullins.microbiol.washington.edu Reviews
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Mullins Lab Computational Biology Software. Uses molecular, computational, and virus biology techniques to provide insights into the relationship between HIV and its human hosts in an effort to fight the AIDS pandemic. Below is a catalog of software we’ve produced during this work to help us and others study retroviruses. Applications marked requires login are currently only available to lab members and our collaborators. Please email us. If you’d like to learn more about them. A platform for the collect...
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2 applications
3 divein
4 methylation station
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6 viroverse
7 tcozy
8 databases
9 hiris
10 primerdb
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Computational Biology Software — Mullins Lab | indra.mullins.microbiol.washington.edu Reviews

https://indra.mullins.microbiol.washington.edu

Mullins Lab Computational Biology Software. Uses molecular, computational, and virus biology techniques to provide insights into the relationship between HIV and its human hosts in an effort to fight the AIDS pandemic. Below is a catalog of software we’ve produced during this work to help us and others study retroviruses. Applications marked requires login are currently only available to lab members and our collaborators. Please email us. If you’d like to learn more about them. A platform for the collect...

INTERNAL PAGES

indra.mullins.microbiol.washington.edu indra.mullins.microbiol.washington.edu
1

Phred decoder ring

https://indra.mullins.microbiol.washington.edu/explain-phred

Paste or type your own Phred 33 encoded quality string. Used by Sanger and new Illumina sequencing) into the input below to decode it. Learn more about Phred quality scores on Wikipedia. Probability of incorrect base call.

2

Sequence Name Reformatter

https://indra.mullins.microbiol.washington.edu/cgi-bin/SeqNameInfoRetriever/seqnameinforetriever.cgi

Upload sequence fasta file. Delimiter(s) used in sequence name. Put all together if there are more than one delimiter. If sequence name is "gi 672892375 gb AIK03017.1 nef protein [Human immunodeficiency virus 1]", the delimiter could be any or combination of ' ', ' ', '.', '[', ']', or even ' .

3

Fitness Experiment Chromatogram Quantitation

https://indra.mullins.microbiol.washington.edu/cgi-bin/chromatquant.cgi

Leader sequences specify the 5' sequence context of the polymorphism; there is no automatic reverse complementation for reverse primers so be sure to enter the sequence in the direction it was recorded. The reported peak heights will be for the position following. The entire match. A. Will match any base, which is useful for ignoring polymorphisms at a position other than the one under consideration.

4

HIV Sequence Locator API

https://indra.mullins.microbiol.washington.edu/locate-sequence

HIV Sequence Locator API. A dead-simple web API for LANL's HIV sequence locator. Providing results in JSON. Positioning, region, and protein information is all available. Most of the data presented in the human-readable HTML page is extracted via this API. Get in touch if you need something that's missing! Requires one or more values for the POST parameter. Parameter as a URL-encoded string or file upload of FASTA. To reverse complement sequences. You should instead take care of this before submitting.

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Computing Help - Mullins Molecular Retrovirology Lab

https://mullinslab.microbiol.washington.edu/help

Mullins Molecular Retrovirology Lab. To request help, please email mullspt@uw.edu. You may also want to peruse the self-service instructions on the wiki.

mullinslab.microbiol.washington.edu mullinslab.microbiol.washington.edu

Mullins Lab Publications

https://mullinslab.microbiol.washington.edu/publications

Mullins Molecular Retrovirology Lab. Select a year: 1995. Smith KN, Mailliard RB, Piazza PA, Fischer W, Korber BT, Fecek RJ, Ratner D, Gupta P, Mullins JI, Rinaldo CR. Effective Cytotoxic T Lymphocyte Targeting of Persistent HIV-1 during Antiretroviral Therapy Requires Priming of Naive CD8 T Cells. Collier AC, Chun TW, Maenza J, Coombs RW, Tapia K, Chang M, Stevens CE, Justement JS, Murray D, Stekler JD, Mullins JI, Holte SE. Proceedings of the National Academy of Sciences of the United States of America.

viroverse.washington.edu viroverse.washington.edu

About Viroverse

https://viroverse.washington.edu/about.html

Dr Mullins (project PI) has long been interested in a structured system to store the data generated and used in his lab. Evaluating commercial systems, he found that none met the needs of investigators looking to include experimental data for molecular biology togther with the results and analysis. Thus began, Viroverse. Viroverse is developed in the laboratory of Jim Mullins. Early stages of development benefited from the involvement of Ram Samudrala.

mullinslab.microbiol.washington.edu mullinslab.microbiol.washington.edu

Site Map - Mullins Molecular Retrovirology Lab

https://mullinslab.microbiol.washington.edu/sitemap.html

Mullins Molecular Retrovirology Lab. HIV Dynamics and Evolution, 2000.

mullinslab.microbiol.washington.edu mullinslab.microbiol.washington.edu

Mullins Lab People

https://mullinslab.microbiol.washington.edu/people

Mullins Molecular Retrovirology Lab. James I. Mullins. Ruth L. Kirschstein. Undergraduate Students ( calendar. Coon (née Stevens), Eva. Eilers, Braiden Laura Celeste Young. Ghosh, Ananta K. He, Xi (CC). Hill, C Alexander. Hong, John K. Leulebirhan, Tsigereda Biru. Mahalanabis, Madhumita (Sonali). Van't Wout, Angélique.

mullinslab.microbiol.washington.edu mullinslab.microbiol.washington.edu

Mullins Lab Protocols

https://mullinslab.microbiol.washington.edu/protocols

Mullins Molecular Retrovirology Lab. Sequence Analysis for Research Genetics Clones. Separation of T-Cell Subsets by FACStar. Measurement of Intracellular Calcium By Flow Cytometry. Chemokine Receptor Expression Assay by Flow Cytometry. FACSCalibur user log sheet. Cell Quest User's Guide. Intracellular p24 Assay by Flow Cytometry (BD). Intracellular p24 Assay by Flow Cytometry (Caltag). Radiolabeled First-Strand cDNA Synthesis. Oligonucleitide Hybridization to Glass Arrays. Hot Asymmetric PCR (Katze Lab).

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Computational Biology Software — Mullins Lab

Mullins Lab Computational Biology Software. Uses molecular, computational, and virus biology techniques to provide insights into the relationship between HIV and its human hosts in an effort to fight the AIDS pandemic. Below is a catalog of software we’ve produced during this work to help us and others study retroviruses. Applications marked requires login are currently only available to lab members and our collaborators. Please email us. If you’d like to learn more about them. A platform for the collect...

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