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URGENT help FASTA on GCG

LIUNI at PLAUTO.CSATA.IT LIUNI at PLAUTO.CSATA.IT
Thu Apr 7 08:38:42 EST 1994


 Hi,

 Could anyone help me for FASTA problem on GCG package?

 Under  is reported my session with Fasta program 

========================  TO ============================================
FASTA does a Pearson and Lipman search for similarity between a
query sequence and any group of sequences.  FASTA answers the
question, "What sequences in the database are similar to my sequence?"
The relationship between FASTA and WORDSEARCH has not been
characterized, but FASTA is faster and, for some searches, more
sensitive.

 FASTA with what query sequence ?  p.seq

                  Begin (* 1 *) ?
                End (*   145 *) ?

 Search for query in what sequence(s) (* GenEMBL:* *) ?  em_fun:*

 What word size (* 6 *) ?

 List how many best scores and alignments (* 40 *) ?

 What should I call the output file (* P.Fasta *) ?

          1 Sequences         378 bp searched    FUN:A00040
        101 Sequences     143,453 bp searched    FUN:ANACUD
        201 Sequences     387,974 bp searched    FUN:ANRRN5G2
        301 Sequences     541,829 bp searched    FUN:BGLJM2957
        401 Sequences     692,327 bp searched    FUN:CARGA2
        501 Sequences     820,461 bp searched    FUN:CFRGSS9B
        601 Sequences     964,109 bp searched    FUN:CMFAHR
        701 Sequences   1,143,649 bp searched    FUN:CTSRRNAB
        801 Sequences   1,201,541 bp searched    FUN:EARRA
        901 Sequences   1,329,199 bp searched    FUN:FJRRNG1
      1,001 Sequences   1,413,149 bp searched    FUN:HARNAITSH
      1,101 Sequences   1,604,775 bp searched    FUN:KLL41A
      1,201 Sequences   1,759,558 bp searched    FUN:LPRRLSAN
      1,301 Sequences   1,856,944 bp searched    FUN:MRRR25SB
      1,401 Sequences   2,053,312 bp searched    FUN:NCLEURSC
      1,501 Sequences   2,223,779 bp searched    FUN:NCSOD1
          .    .            .        .               .
          .    .            .        .               .
          .    .            .        .               .


(Nucleotide) FASTA of: P.Seq  from: 1   to: 145  April 6, 1994  15:02
 TO: em_fun:*  Sequences:      5,097  Symbols:  9,889,085  Word Size: 6


Score Init1 Initn
<  4   126   126:==================================================
   8     0     0:
  12     0     0:
  16     0     0:
  20     0     0:
  24   556   556:==================================================
  28  1093  1093:==================================================
  32  2320  2320:==================================================
  36  2626  2626:==================================================
  40  1600  1600:==================================================
  44   804   804:==================================================
  48   524   517:==================================================
  52   297   288:==================================================
    56   137   126:==================================================
  60    65    59:==============================---
  64    32    31:================
  68     9     9:=====
  72     3     3:==
  76     1    10:=++++
  80     1    12:=+++++
  84     0     3:++
  88     0     4:++
  92     0     2:+
  96     0     0:
 100     0     2:+
 104     0     1:+
 108     0     1:+


 mean initn score:  34.2 (6.58)
 mean init1 score:  34.2 (6.58)


The best scores are:                                        init1 initn opt


 *** Error: Cannot open file FUN:SCCHROMI


 *** Error: Cannot open file FUN:SCCHRIII


 *** Error: Cannot open file FUN:SCCIIORF


 *** Error: Cannot open file FUN:SCIIL26O


 *** Error: Cannot open file FUN:SCCHRIII
 ============================== FROM ====================

 What is the cause of this error ?

 Thanks in advance 

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
^ Dr.Sabino LIUNI                                                       ^
^                                                                       ^
^ Administrator for The Italian EMBNet node                             ^
^                                                                       ^
^ Tel: XX-39-80-5482130               Area di Ricerca CNR               ^
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^                                     70126 Bari - Italy                ^ 
^                                                                       ^
^ LIUNI at MVX36.CSATA.IT                                                  ^
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