| Include Page | ||||
|---|---|---|---|---|
|
The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
EMBOSS matcher
matcher identifies local similarities in two input sequences using a rigorous algorithm based on Bill Pearson's lalign application, version 2.0u4 (Feb. 1996). The substitution matrix, gap insertion and extension penalty are specified. The specified number of top-scoring pair-wise local sequence alignments are written to file.
Quick Start
To use matcher,
- upload your Two input sequence data in most format, such as fasta, GenBank, Embl, or Emsembl, gcg formats.
- launch your job
- Resource: More information on input sequence feature and format could be found at https://pods.iplantcollaborative.org/wiki/display/sciplant/EMBOSS+Sequence+Feature+Format
Test Data
Input File
The input can be in most sequence format, such as fasta, gcg, GenBank, Embl, and Ensembl formats. For details, please see http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/seqret.html
- Test input in GenBank sequence format: Community Data -> iplantcollaborative -> example_data ->EMBOSS ->Input -> hha_human.txt and hhb_human.txt
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Default parameters only, no further configuration needed.
Output File(s)
Standard EMBOSS output report file.
- Expected output files: Community Data -> iplantcollaborative -> example_data -> EMBOSS -> Output -> matcher.output
Tool Source
...