National Heart, Lung, and Blood Institute

Epithelial Systems Biology Laboratory (ESBL)

Knepper Laboratory

Computational Tools

The ESBL has developed a number of software tools that can be accessed at the links below:

  • AbDesigner - a tool for choosing optimal peptide sequences to be used to produce antibodies.
  • CPhos - information theory-based algorithm to assess the conservation of phosphorylation sites among species.
  • PhosphoLogo - a tool that uses information theory to generate sequence logos from a list of peptide sequences surrounding a phosphorylated residue.
  • PTM Centralizer - a tool that converts MS-identified peptides containing a specific feature (e.g. a phosphorylation site) to sequences of given length with the feature in the center.
  • PhosSA - a program for phosphorylation site assignment in LC-MS/MS data.
  • ProMatch - a program to match peptide sequences to entries in NCBI Reference Sequence (RefSeq) Protein Database.
  • Temporal Pattern Mining (TPM) algorithm - a tool that clusters time-series data sets according to time-course pattern.
  • Automated Bioinformatics Extractor (ABE) - a batch tool for extraction of specified information about specific proteins from UniProt or RefSeq protein records.
  • Conditional Allele Mouse Planner (CAMP) - a tool for designing protocols for breeding transgenic and knockout mice with cost estimation.
  • Renal Inner Medulla Free-Energy Calculator - a tool for calculation of net free energy change in steady-state models of the renal concentrating mechanism.

  • Go to Proteomics and Transcriptomics Databases

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