EMBOSS explorer

esim4

Align an mRNA to a genomic DNA sequence (read the manual)

Unshaded fields are optional and can safely be ignored. (hide optional fields)

Input section

Select an input sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:

Genomic sequence. Use one of the following three fields:

  1. To access a sequence from a database, enter the USA here:
  2. To upload a sequence from your local computer, select it here:
  3. To enter the sequence data manually, type here:
Additional section
Sets the word size (W) for blast hits. Default value: 12.
Sets the word extension termination limit (X) for the blast-like stage of the algorithm. Default value: 12.
Sets the cutoff (E) in range [3,10].
False: esim4 calculates mspA, True: value from mspA command line argument.?
MSP score threshold (K) for the first stage of the algorithm.
False: esim4 calculates mspB, True: value from mspB command line argument.?
MSP score threshold (C) during the second stage of the algorithm.
Weight value (H) (undocumented). 0 uses a default, >0 is a value
Bound (K) for the diagonal distance within consecutive MSPs in an exon.
Align mRNA to specified (R) genome strand(s).
Output format (A)
Trim poly-A tails (P)?
Search for small marginal exons (N)?
Disallow ambiguity characters (B)?
Define CDS ends in mRNA (S)
Undocumented (f) - some sort of offset in first sequence.
Undocumented (F) - some sort of offset in second sequence.
Undocumented (t)- offset end of first sequence?
Undocumented (T) - offset end of second sequence?
Output section
Run section
Email address: If you are submitting a long job and would like to be informed by email when it finishes, enter your email address here.