STAMP 4.4.2 – Structural Alignment of Multiple Proteins

STAMP 4.4.2

:: DESCRIPTION

STAMP is a package for the alignment of protein sequences based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit’ superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. If you are after a multiple sequence alignment for proteins of unknown 3D structure, stop reading now and contact GJB for information about AMPS, which can be used to perform multiple sequence alignments, or see www.jalview.org for GJB’s latest methods for this problem.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Window with Cygwin
GCC

:: DOWNLOAD

STAMP

:: MORE INFORMATION

Citation

Proteins. 1992 Oct;14(2):309-23.
Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels.
Russell RB1, Barton GJ.

STAMP 1.1 – Tool-kit for DNA Motif Comparison

STAMP 1.1

:: DESCRIPTION

STAMP is a newly developed web server that is designed to support the study of DNA-binding motifs. STAMP may be used to query motifs against databases of known motifs; the software aligns input motifs against the chosen database (or alternatively against a user-provided dataset), and lists of the highest-scoring matches are returned. Such similarity-search functionality is expected to facilitate the identification of transcription factors that potentially interact with newly discovered motifs.

:: DEVELOPER

Benos Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

STAMP

:: MORE INFORMATION

Citation:

S Mahony, PV Benos,
“STAMP: a web tool for exploring DNA-binding motif similarities“,
Nucleic Acids Research (2007) 35(Web Server issue):W253-W258.

STAMP 2.1.3 – Analyze Metagenomic Profiles

STAMP 2.1.3

:: DESCRIPTION

STAMP (Statistical Analysis of Metagenomic Profiles) is a software package for analyzing metagenomic profiles (e.g., a taxonomic profile indicating the number of marker genes assigned to different taxonomic units or a functional profile indicating the number of sequences assigned to different biological subsystems or pathways) that promotes ‘best practices’ in choosing appropriate statistical techniques and reporting results. It encourages the use of effect sizes and confidence intervals in assessing biological importance. A user friendly, graphical interface permits easy exploration of statistical results and generation of publication quality plots for inferring the biological relevance of features in a metagenomic profile.

::DEVELOPER

Beiko lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac OsX / Linux

:: DOWNLOAD

STAMP

:: MORE INFORMATION

Citation

STAMP: statistical analysis of taxonomic and functional profiles.
Parks DH, Tyson GW, Hugenholtz P, Beiko RG.
Bioinformatics. 2014 Jul 23. pii: btu494.

Parks, D.H. and Beiko, R.G. (2010).
Identifying biologically relevant differences between metagenomic communities.
Bioinformatics, 26, 715-721.

STAMP 1.1 – Microsatellite Marker Design Extension for the Staden package

STAMP 1.1

:: DESCRIPTION

STAMP is a Staden package extension for automating microsatellite marker design. It integrates the de novo repeat identification program Phobos by Christoph Mayer and PRIMER3 into Pregap and Gap4. It allows tagging repeats for masking them out for assembly (Pregap), finding repeats in assembled Gap4 databases, automatic primer design flanking marked repeats and multiplex primer design.

::DEVELOPER

Christoph Mayer

:: SCREENSHOTS

:: REQUIREMENTS

Linux/MacOsX / Windows
Staden

:: DOWNLOAD

STAMP

:: MORE INFORMATION

Citation

Kraemer, L., Beszteri, B., Gäbler-Schwarz, S., Held, C., Leese, F., Mayer, C., Pöhlmann, K. & Frickenhaus, S (2009)
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design.
BMC Bioinformatics 10:41.