GCG vs EMBOSS

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GCG vs EMBOSS

• Gary Williams

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Which is better GCG or EMBOSS?

• You must decide for yourselves
• You may find other packages that do what you want
• Use the tools that do the job
• This is a comparison of GCG and EMBOSS to help
  you decide

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Interfaces

• Web
• W2H available for both
• EMBOSS W2H still has rough edges
• PISE
• Others under development
• X-Windows
• GCG - Seqlab
• EMBOSS - SPIN, ( others coming)
• Telnet/xterm/Character-based
• emnu

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Command line is very similar

• The UNIX command line interfaces of GCG and
  EMBOSS are very similar.
• You type the name of the program
• You can add any options you want to the
  command-line
• Press the RETURN key
• Any mandatory information that was not on the
  command-line will be prompted for.

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GCG command-line

• name -otherthing
• This is the name program that reads a sequence
  and writes out something.
• NAME what sequence ? emblhsfau1
• Begin ( 1 ) ?
• End ( 2016 ) ?
• Reverse ( No ) ?
• What should I call the output (
  hsfau.name ) ?

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EMBOSS command-line

• name -other thing
• Reads in sequences and writes a thing
• Input sequence(s) emblhsfau1
• Output data hsfau1.name
• Use -ask to make EMBOSS programs prompt for the
  start and end of sequences

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Some common options

• Running in scripts, dont prompt, just fail if
  command-line is insufficient
• GCG -default
• EMBOSS -auto
• Help on options
• GCG -check
• EMBOSS -help or -help -verbose
• Boolean options (Yes/No, True/False)
• GCG -thing, -nothing
• EMBOSS -thing, -nothing, -thingT, -thingF,
  -thing1, -thing0, -thingY, -thingN

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Sequence options in EMBOSS

• "-sequence" related qualifiers
• -sbegin integer first base used
• -send integer last base
  used, defseq length
• -sreverse bool reverse (if
  DNA)
• -sask bool ask for
  begin/end/reverse
• -slower bool make lower
  case
• -supper bool make upper
  case
• -sformat string input sequence
  format
• -ufo string UFO
  features

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Sequence options in EMBOSS

• "-outseq" related qualifiers
• -osformat string output sequence
  format
• -ossingle bool separate file
  for each entry

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EMBOSS general options

• -debug bool write debug output to
  program.dbg
• -auto bool turn off prompts
• -stdout bool write standard output
• -filter bool read standard input,
  write standard output
• -options bool prompt for required and
  optional values
• -verbose bool report some/full command
  line options
• -help bool report command line
  options

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Data files

• GCG uses .. to divide comments from data
• EMBOSS does not use ..
• In general, EMBOSS uses to mark a comment
  line
• Use embossdata to extract and check on data
  files.
• As in GCG, data files copied into the current or
  home directory are used in preference to the
  originals.

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List files (files of file names)

• Similar to GCG lists files, but no ..
• Comment lines start with
• Can contain the names of other list files
• This is my list file
• emblhsfau
• emblggg
• myfile.seqclone10
• file.seq
• _at_list2

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File formats

• GCG
• only GCG format, MSF and RSF
• EMBOSS
• many formats
• automatically recognised
• can specify using or -osf
• eg
• clustalglobin.aln
• -osf gcg

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One file, many sequences

• GCG
• Only one sequence per GCG file
• EMBOSS
• One or more sequences per file
• Default is to write all sequences to one file
• -ossingle will change to writing many files
• GCG, Staden and plain format files can only hold
  one sequence per file.

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Features

• GCG
• No concept of feature tables
• EMBOSS
• Many programs now write out results as GFF
• Soon, all programs that find things will write
  the results as GFF
• GFF will become another sequence format
• Programs to manipulate and display sets of
  features are planned
• c.f. showfeat, coderet, maskfeat, diffseq

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Databases

• EMBOSS is poor at grouping many databases under
  one name
• E.G. Need a way of referring to embl and
  emblnew as one database.
• This will be done, but currently, a list file
  containing the following seems best
• embl
• emblnew

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Command line wildcards

• GCG
• embl - no problem
• EMBOSS
• embl - UNIX complains it cant find the files
• solution is to quote it
• embl
• or
• embl\

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HELP

• GCG
• genman, genhelp
• EMBOSS
• tfm

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What program does what?

• See David Martins list of equivalences
• http//www.no.embnet.org/Programs/SAL/EMBOSS/fromG
  CG.php3
• NB this doesnt list EMBOSS programs with no
  equivalent in GCG!

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What EMBOSS does NOT do

• The major deficiencies in the EMBOSS package are
• BLAST, FASTA, ASSEMBLY
• You should use the publicly available software
• Blast - NCBI, HGMP, many other sites
• Fasta - HGMP
• Assembly - Staden package

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What EMBOSS does do

• Giving stdout as the output file name makes
  output go to the screen.
• Much effort is put into removing arbitrary
  limits.
• E.g. Max. sequence length 2Gb
• Many programs limited only by available memory
• Source code available for inspection, change and
  writing your own programs
• EMBOSS is FREE!
• GNU Public Licence
• Open Source Software

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THE END