pegi3s/emboss repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image allows the usage of the EMBOSS⁠ suite. Popular applications in this suite are⁠:

• getorf: Find and extract open reading frames.
• prophet: Gapped alignment for profiles.
• infoseq: Displays some simple information about sequences.
• water: Smith-Waterman local alignment.
• pepstats: Protein statistics.
• showfeat: Show features of a sequence.
• palindrome: Looks for inverted repeats in a nucleotide sequence.
• eprimer3: Picks PCR primers and hybridization oligos.
• profit: Scan a sequence or database with a matrix or profile.
• extractseq: Extract regions from a sequence.
• marscan: Finds MAR/SAR sites in nucleic sequences.
• tfscan: Scans DNA sequences for transcription factors.
• patmatmotifs: Compares a protein sequence to the PROSITE motif database.
• showdb: Displays information on the currently available databases.
• wossname: Finds programs by keywords in their one-line documentation.
• abiview: Reads ABI file and display the trace.
• tranalign: Align nucleic coding regions given the aligned proteins.

To obtain the help of an application, you just need to run: docker run --rm pegi3s/emboss <emboss-application-name> -h (e.g. docker run --rm pegi3s/emboss prophet -h)

⁠Using the EMBOSS image in Linux

To run an application, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/emboss <emboss-application-name> <options>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <emboss-application-name> to the name of the EMBOSS application you want to use.
• <options> with the specific options of the EMBOSS application. These options will include the input/output files, which should be referenced under /data/.