EMBOSS
From Wiki CEINGE
EMBOSS (European Molecular Biology Open Software Suite) is a software analysis package developed for the needs of molecular biologists. The software is Open Source, thus allowing other scientists to develop and release new software, integrating also many other available packages and tools for sequence analysis.
EMBOSS (verison 3.0) is installed and runs on the cluster server.
[edit] How to reach and use EMBOSS
- EMBOSS applications can be searched and launched from the main website or through the PROGsDB.
- Most EMBOSS applications can be directly launched by CAPRI.
- In the VLS environment, the EMBOSS package is fully available for command line use in the directory /bioprogs/emboss.
[edit] Available programs
- More than one hundred of programs (called applications) are collected within EMBOSS, covering different biological areas such as:
- Protein motif identification and domain analysis
- Nucleotide sequence pattern analysis
- Sequence alignment
- Presentation tools for publication
- and much more.
- The EMBOSS applications are organized into groups according to their function (see the Application Groups Documentation for more information).
- The complete list of installed EMBOSS applications is available here
- Some frequently used applications are:
- matcher: Perform a local alignment of two sequences.
- pepstats: Perform several statistics on proteins.
- showfeat: Show features of a sequence.
- patmatmotifs: Compares a protein sequence to the PROSITE motif database.
- abiview: Reads ABI file (electropherograms) and display the trace.
- palindrome: looks for inverted repeats in a nucleotide sequence.
- infoseq: Displays some simple information about sequences.
- water: Perform a local alignment of two sequences according to the Smith-Waterman algorithm.
- needle: Perform a global alignment of two sequences according to the Needleman-Wunsch algorithm.
- eprimer3: Picks PCR primers and hybridization oligos on sequences.
- extractseq: Extract regions from a sequence.
- tfscan: Scans DNA sequences for transcription factors.
- tranalign: Align nucleic coding regions given the aligned proteins.
[edit] References
- Rice P, Longden I and Bleasby A EMBOSS: The European Molecular Biology Open Software Suite Trends in Genetics, 2000, 16:276-277.
- For more details about EMBOSS, visit the EMBOSS web site
