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EST2GENOME : Align EST and genomic DNA sequences (EMBOSS)



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input Section


advanced Section


output Section


input Section


EST sequence(s) (-est) : please enter
either :
  1. the name of a file:
  2. or the actual data here:

(sequence format)


Genomic sequence (-genome) : please enter either :

  1. the name of a file:
  2. or the actual data here:

(sequence format)


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advanced Section

Score for matching two bases (-match)
Cost for mismatching two bases (-mismatch)
Gap penalty (-gappenalty)
Intron penalty (-intronpenalty)
Splice site penalty (-splicepenalty)
Minimum accepted score (-minscore)
Reverse orientation (-reverse)
Use donor and acceptor splice sites (-splice)
Comparison mode (-mode)
Print out only best alignment (-best)
Space threshold (in megabytes) (-space)
Shuffle (-shuffle)
Random number seed (-seed)

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output Section

outfile (-outfile)
Show the alignment (-align)
Alignment width (-width)

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Some explanations about the options


input Section
enter either the name of a file or the actual data
if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button)
OR you can type your data in the next area, or cut and paste it from another application.
(but not both)

advanced Section
Gap penalty (-gappenalty)
Cost for deleting a single base in either sequence, excluding introns
Intron penalty (-intronpenalty)
Cost for an intron, independent of length.
Splice site penalty (-splicepenalty)
Cost for an intron, independent of length and starting/ending on donor-acceptor sites
Minimum accepted score (-minscore)
You can exclude alignments with scores below a threshold by setting this to be false.
Reverse orientation (-reverse)
Reverse the orientation of the EST sequence
Use donor and acceptor splice sites (-splice)
Use donor and acceptor splice sites. If you want to ignore donor-acceptor sites then set this to be false.
Comparison mode (-mode)
This determines the comparion mode. The default value is 'both', in which case both strands of the est are compared assuming a forward gene direction (ie GT/AG splice sites), and the best comparsion redone assuming a reversed (CT/AC) gene splicing direction. The other allowed modes are 'forward', when just the forward strand is searched, and 'reverse', ditto for the reverse strand.
Print out only best alignment (-best)
You can print out all comparisons instead of just the best one by setting this to be false.
Space threshold (in megabytes) (-space)
for linear-space recursion. If product of sequence lengths divided by 4 exceeds this then a divide-and-conquer strategy is used to control the memory requirements. In this way very long sequences can be aligned.
If you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine's physical RAM)

output Section
Show the alignment (-align)
Show the alignment. The alignment includes the first and last 5 bases of each intron, together with the intron width. The direction of splicing is indicated by angle brackets (forward or reverse) or ???? (unknown).
Sequence format
The sequence will be automatically converted in the format needed for the program
providing you enter a sequence either:
in plain (raw) sequence format or in one of the following known formats:
IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW
You may enter in the text area a database entry code, or an accession number, in this form:
database:entry_name
or:
database:accession.

Pise form generator version: 5.a (16 Dec 2002 11:54)