[EMBOSS] How to apply the einverted and etandom to a fasta file

[yun zheng]

Hi,

I am a new user of emboss. I am trying to find repeat sequences in a
nucleotide sequence file that have many sequences.

Can anybody tell me how to use einverted and etandem to analyze all the
sequences in a fasta file?

Many Thanks.

Sincerely

Zheng, yun

Dept of Computer Science and Engineering

Washington Univ in St Louis

Campus Box 1045

1 Brookings Drive

Jolley Hall 505

St Louis, MO 63130



Details:

I install a version on the linux platform. And the command is like follows,
where the default value is used.

>einverted -sequence test.fasta -outfile test.outfile -outseq
>test-i.fasta

Finds DNA inverted repeats

Gap penalty [12]:

Minimum score threshold [50]:

Match score [3]:

Mismatch score [-4]:



But the output file seems always to be empty.



When I try etandom

>etandem -sequence test.fasta -outfile test-t.out -origfile test.etandem

Looks for tandem repeats in a nucleotide sequence

Minimum repeat size [10]:

Maximum repeat size [10]: 18

However, it seems that only the first sequence is analyzed by the einverted
and etandom. The test-t.out file is as follows.

########################################

# Program: etandem

# Rundate: Sat Oct 28 2006 17:24:30

# Commandline: etandem

#    -sequence test.fasta

#    -outfile test-t.out

#    -origfile test.etandem

#    -maxrepeat 18

# Report_format: table

# Report_file: test-t.out

########################################



#=======================================

#

# Sequence: D9X6RJV01EER0J     from: 1   to: 55

# HitCount: 0

#

# Threshold: 20

# Minrepeat: 10

# Maxrepeat: 18

# Mismatch: No

# Uniform: No

#

#=======================================

   Start     End   Score   Size  Count Identity Consensus

#---------------------------------------

#---------------------------------------

 Many thanks.