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GL SPERVEDYGR THRGHHHHRH RRCSRKR

Global alignments created by PileUp in Version 9. 


  51 RHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK....... 93    

                                           |.  :

   1 ......................................MVRYRMRSPSEG 12
Global alignment created by Gap in Version 9.

Pileup doesn't find conserved motifs in my alignment in Version 9

The following information is taken from the GCG Newsletter, July 1997.

PileUp was always intended as a global alignment tool, which aligns sequences along their entire lengths. Because of this, PileUp is not ideally suited to finding the best local region of similarity (such as a shared motif) among all of the sequences. Global alignment algorithms tend to overlook areas of local similarity in favor of aligning the entirety of all sequences.

If you know where the areas of conserved motifs lie, use the SeqLab Editor to manually edit the resulting global alignment from PileUp, and then select subranges to realign portions of an existing alignment.

References

(1) Henikoff, S. and Henikoff, J. G. 1992. Amino acid substitution matrices from protein blocks. Proceedings of the National Academy of Sciences USA 89, 10915-10919.

(2) Schwartz, R.M. and Dayhoff, M.O. (1979). Matrices for Detecting Distant Relationships. In Atlas of Protein Sequences and Structure, (M.O. Dayhoff, ed.), 5, Suppl. 3 (pp; 353-358), National Biomedical Research Foundation, Washington, D.C., USA.

How do I run blast searches in batch mode?

After NCBI replaced their experimental blast servers in Jan 98, the blast searches on the helix system changed. The new blast program does not have the 'blast -batch' command. Instead, you should use the helix utility batchblast. A simple run of batchblast would be 
helix% batchblast *.seq
which would run blast searches with default parameters f