EMBOSS can read and write sequences in all the common sequence formats, such as EMBL, Genbank, Fasta, SwissProt, PIR, GCG, MSF, Clustal and raw. Thus, when using EMBOSS, sequences do not have to be converted from one format to another.

Some of the areas covered by EMBOSS programs:

• Sequence Alignment
• Rapid database searching with sequence patterns
• Protein motif identification, including domain analysis
• Nucleotide sequence pattern analysis, for example to identify CpG islands or repeats
• Codon usage analysis for small genomes
• Rapid identification of sequence patterns in large scale sequence sets
• Presentation tools for publication
• And much more

Version

How to Use

• For short infrequent jobs, use the EMBOSS web interface on Helixweb.
• For longer jobs or larger numbers of sequences, use EMBOSS on Helix. Type 'emboss' at the command prompt (once per session) to initialize EMBOSS, then the name of the EMBOSS application:

helix% emboss
helix% application name (e.g. seqret)

	    

A more detailed sample session is at the end of this page.
Note: For sequence editing, we recommend the Seaview editor. RSF multiple sequence alignment files (from the GCG program) can be converted to MSF files and viewed/edited via Seaview. See the Seaview page for more information.
• For large-scale usage (1000s of sequences), EMBOSS is also available on Biowulf

Documentation

• EMBOSS online documentation -- documentation for all EMBOSS programs.
• EMBOSS program groups by function.
• The online tutorial maintained by David Martin at the EMBOSS sourceforge site.
• Equivalent programs in Emboss & GCG to help users migrating from GCG to EMBOSS.
• List and update status of all EMBOSS databases on the Helix Systems.
• Type 'wossname' to search for programs by keyword (e.g. 'wossname restriction' to search for programs related to restriction enzymes.
• Type 'showdb' to display available databases
• Type 'tfm' to displays a program's help documentation manual (e.g. 'tfm digest')
• Type 'program -h' for help in command line qualifiers (e.g. 'pepcoil -h')

Sample Session

helix% emboss

************************************************************************
                     Welcome to EMBOSS 4.0.0
************************************************************************

Databases available: 
  genbank             Release 167 (19/Aug/08)
  genpept             Release 167 (27/Aug/08)
  est                 Release 167 (19/Aug/08)
  refseqaa            Release 30 (11/Jul/08)
  refseqnt            Release 30 (11/Jul/08)
  PROSITE             Release 20.36 (22/Jul/08)
  Restriction Enzymes (REBASE) 809 (29/Aug/08)
  Transfac            Release 11.4 (14/Dec/07)
  prints              Release 38_1 (24/Oct/07)
  uniprot             Release 14.0 (22/Jul/08)
  allnt               including genbank,est,refseqnt,gbnew
  allaa               including genpept,uniprot,refseqaa,gpnew
  gpnew               01/Sep/08, 61516 entries since 19/Aug/08 rel 167
  gbnew               31/Aug/08, 403077 entries since 19/Aug/08 rel 167

     Type 'wossname keyword' to find a program
     Type 'showdb' to display available databases
     Type 'tfm programname' to display the program help
     Type 'programname -help' to list command-line options

     EMBOSS Web Interface at NIH: http://helixweb.nih.gov/emboss/

     HELP! Helix Staff: 301-594-6248 or email: staff@helix.nih.gov
*********************************************************************

helix% needle maize_hb.fas rice_hb.fas 
Needleman-Wunsch global alignment.
Gap opening penalty [10.0]: 
Gap extension penalty [0.5]: 
Output alignment [af291052.needle]: 

helix% more af291052.needle
########################################
# Program: needle
# Rundate: Mon Jan 08 2007 15:59:43
# Commandline: needle
#    [-asequence] maize_hb.fas
#    [-bsequence] rice_hb.fas
# Align_format: srspair
# Report_file: af291052.needle
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: AF291052.1
# 2: OSU76029
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 958
# Identity:     607/958 (63.4%)
# Similarity:   609/958 (63.6%)
# Gaps:         207/958 (21.6%)
# Score: 2034.5
# 
#
#=======================================

AF291052.1         1 ATGGCACTCGCGGAGG---CCGACGACGGCGCGGTGGTCTTCGGCGAGGA     47
                     |||||.||||.|||||   .|.|.|.||..||||||..||||.|||||||
OSU76029           1 ATGGCTCTCGTGGAGGATAACAATGCCGTAGCGGTGAGCTTCAGCGAGGA     50

AF291052.1        48 GCAGGAGGCGCTGGTGCTCAAGTCGTGGGCCGTCATGAAGAAGGACGCCG     97
                     ||||||||||||||||||||||||.|||||..||.||||||||||..|||
OSU76029          51 GCAGGAGGCGCTGGTGCTCAAGTCATGGGCGATCTTGAAGAAGGATTCCG    100

AF291052.1        98 CCAACCTGGGCCTCCGCTTCTTCCTCAAGTAAGTACGTTTCCGTGCTACA    147
                     ||||..|.|.|||||||||||||.|.|||||.||||  .|.||||.|   
OSU76029         101 CCAATATTGCCCTCCGCTTCTTCTTGAAGTATGTAC--ATGCGTGTT---    145

AF291052.1       148 CACTGCC-----------TGCG----CACGTGCGCTTGGGTT------GC    176
                      |||.||           ||||    ||   |.|.|||||||      ||
OSU76029         146 -ACTACCATTTCTCTTTTTGCGGAATCA---GAGATTGGGTTTGTGAAGC    191

AF291052.1       177 ACCTGCACCGGCGGCCATCGAGC-----------CTGCTCCTTGACTAAC    215
                     |  |..|         ||.||||           |||.|.|.||..|   
OSU76029         192 A--TTAA---------ATTGAGCAATGCATTTCGCTGATACATGTGT---    227

[...]
#---------------------------------------