Pratt 2.1 – Find Flexible Patterns in Unaligned Protein Sequences

Pratt 2.1

:: DESCRIPTION

PRATT is a tool to discover patterns that are conserved in a set of protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported.

Pratt Online Version

::DEVELOPER

Inge Jonassen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Pratt

:: MORE INFORMATION

Citation

I.Jonassen, J.F.Collins, D.G.Higgins.
Finding flexible patterns in unaligned protein sequences
Protein Science 4, 1587-1595 (1995)

I. Jonassen
Efficient discovery of conserved patterns using a pattern graph.
CABIOS 13, 509-522 (1997).

PexSPAM 1.2 – Protein Sequence Feature Extraction

PexSPAM 1.2

:: DESCRIPTION

PexSPAM is a Java standalone program that I wrote for protein sequence feature extraction. PexSPAM was originally designed to be a “feature factory” for secondary structure classification problem in integral membrane proteins. PexSPAM extends the SPAM (Ayres et al, 2002) method by incorporating gap and regular expression constraints into mining procedure.

::DEVELOPER

Joshua Ho

:: SCREENSHOTS

:: REQUIREMENTS

Windows / MacOs / Linux / Unix
Java

:: DOWNLOAD

PexSPAM for Win , Source Code

:: MORE INFORMATION

Citation:

Ho J, Lukov L, Chawla S (2005)
Sequential Pattern Mining with Constraints on Large Protein Databases.
In Chakrabarti S, Sudarshan S, Radha Krishnan P (Eds) Proceedings of the 12th International Conference on Management of Data (COMAD 2005b), 89-100.

ORFer 1.3.2.2 – Retrieval of Protein Sequences and Open Reading Frames from GenBank

ORFer 1.3.2.2

:: DESCRIPTION

ORFer (Open Reading Frame Retrieval) reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.The open reading frame corresponding to the protein sequences is extracted from the XML and displayed. ORFer has a database interface that allows for storing the retrieved sequences in a local SQL database.

::DEVELOPER

Konrad Büssow and Steve Hoffmann

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOSX
Java

:: DOWNLOAD

ORFer

:: MORE INFORMATION

Citation

Konrad Büssow , Steve Hoffmann and Volker Sievert
ORFer – retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files
BMC Bioinformatics 2002, 3:40doi:10.1186/1471-2105-3-40

Alignment Benchmark – Collection of Protein Sequence Alignment Benchmarks

Alignment Benchmark

:: DESCRIPTION

Alignment Benchmark is a collection of protein sequence alignment benchmarks including BALIBASE v3, PREFAB v4, OXBENCH, and SABRE. These have been converted to a standard FASTA format that is convenient for further analysis. Accuracy scores for some selected methods are included to allow third party verification of my results.

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Alignment Benchmark

:: MORE INFORMATION

Citation

A paper is in submission. For now you can cite this URL: Edgar, R.C., http://www.drive5.com/bench.

DASher 1.3.4 – Protein Sequence Client for DAS

DASher 1.3.4

:: DESCRIPTION

DASher is a Java DAS (the Distributed Annotation System) client for displaying annotations on a protein sequence. Enter a protein ID and DASher automatically gathers information about it from DAS servers around the world.

::DEVELOPER

David N. Messina (David.Messina@sbc.su.se) and Erik L. L. Sonnhammer

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / Mac OsX
Java

:: DOWNLOAD

DASher

:: MORE INFORMATION

Citation:

David N. Messina and Erik L. L. Sonnhammer
DASher: a stand-alone protein sequence client for DAS, the Distributed Annotation System
Bioinformatics (2009) 25 (10): 1333-1334.

SPICE 0.9 – Protein Sequences, Structures & Annotations Browser

SPICE 0.9

:: DESCRIPTION

SPICE is a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information.

::DEVELOPER

Andreas Prlic, Thomas Down, Tim Hubbard.

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / Mac OsX
Java

:: DOWNLOAD

SPICE

:: MORE INFORMATION

Citation:

Adding some SPICE to DAS
Bioinformatics Volume 21, suppl_2 Pp. ii40-ii41
Andreas Prlic, Thomas A. Down and Tim J. P. Hubbard