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BOXSHADE server trouble shooting


If you receive no output (you get a page saying 'here is your output' but clicking there only gives an error message) the problem is usually due to a non-recognized input format.

The BOXSHADE program on the server only recognizes:

  • MSF format as written by GCG programs or by READSEQ

  • ALN format as written by ClustalV or ClustalW

  • other formats understood by READSEQ. These files must be pre-aligned, boxshade is doing no multiple alignment. When using READSEQ-compatible formats, choose "other formats" as the format-specifier

Note:The current version does NOT recognize MSF format as written by ClustalW.

Note:When using the ClustalW server at BCM, use the FASTA-format part of the output and choose 'other formats' in the format menu.

When using MSF or ALN files, only complete files are acceptable, the first line must be the header line (which usually contains either the word MSF or Clustal) Make sure that there are no additional blank lines at the top or the bottom of the input field.

And don't forget to tell the program, which format you use!


Here are two examples: The first one is an MSF file (written by READSEQ)

-------------------------- cut here -------------------------------------- 
 test.msf  MSF: 20  Type: N  January 01, 1776  12:00  Check: 7596 ..

 Name: Seq1             Len:    20  Check:  5696  Weight:  1.00
 Name: Seq2             Len:    20  Check:  6211  Weight:  1.00
 Name: Seq3             Len:    20  Check:  5689  Weight:  1.00
//

           Seq1  GTSAGILPER THKKNMIE..
           Seq2  GSS.GLLPEK THRRNMIELY
           Seq3  GTTGGAAPSK THSRNMIDAI
-------------------------- cut here -------------------------------------- 


The second example is an ALN file written by ClustalW

-------------------------- cut here -------------------------------------- 
CLUSTAL W(1.5) multiple sequence alignment

Seq1            GTSAGILPERTHKKNMIE..
Seq2            GSS.GLLPEKTHRRNMIELY
Seq3            GTTGGAAPSKTHSRNMIDAI
                *.. *  * .** .***.  
-------------------------- cut here --------------------------------------