Pairwise Alignments

By default, SCANPS will output a single paiwise alignment (two-sequence alignment) between the query sequence and each database sequence in the score list. For example:

# Start_Alignments_Rank: 1
# Query: SCANPS_TEST Target: ANX3_RAT Number_of_Alignments: 1
# Target_Title: (P14669) Annexin III (Lipocort
# N: 1 Raw_Score: 450 Query_Length: 74 Target_Length: 324 Evalue: 1.9793e-20
        *****************.**************************. ****
      1 YPGFNPSVDAEAIRKAIRGIGTDEKTLINILTERSNAQRQLIVKQYQEAY      50
     16 YPGFNPSVDAEAIRKAIKGIGTDEKTLINILTERSNAQRQLIVKHIQEAY      65

        ************************
     51 EQALKADLKGDLSGHFEHVMVALI      74
     66 EQALKADLKGDLSGHFEHVMVALI      89

# End_N: 1
# End_Alignments_Rank: 1

# Start_Alignments_Rank: 2
# Query: SCANPS_TEST Target: ANX3_MOUSE Number_of_Alignments: 1
# Target_Title: (O35639) Annexin III (Lipocort
# N: 1 Raw_Score: 439 Query_Length: 74 Target_Length: 323 Evalue: 9.29946e-20
        ****.**************.*************************** **
      1 YPGFNPSVDAEAIRKAIRGIGTDEKTLINILTERSNAQRQLIVKQYQEAY      50
     15 YPGFSPSVDAEAIRKAIRGLGTDEKTLINILTERSNAQRQLIVKQYQAAY      64

        ** ** *****************.
     51 EQALKADLKGDLSGHFEHVMVALI      74
     65 EQELKDDLKGDLSGHFEHVMVALV      88

# End_N: 1
# End_Alignments_Rank: 2

Each alignment is contained within a pair of ``Start_Alignments'' and ``End_Alignments'' labels. The rank of the alignment is also shown. The line beginning ``# N: 1'' idenifies this as the first alignment for this pair of sequences. SCANPS can output more than one alignment for each pair of sequences, so this allows these to be separated and parsed in the output. The pairwise alignment is output in a fairly conventional way with the ``-'' character used to denote gaps. The line above the alignment shows ``*'' for identities and ``.'' for pairs of amino acids that score positive in the pairscore matrix that was used in the search.

There are various ways to control this pairwise output. For example, the number of residues per line can be modified with the -output_len command line option.

You can adjust how many alignments you want to see by using the -aptt and -max_aout commands. These work in a similar way to the -nptt and -max_nout described above. For example to only output the first 20 alignments rather than alignments for every pair shown in the score list do:

-aptt 0 -max_aout 20

Often one want so suppress pairwise alignments entirely. You can do this with:

-aptt 0 -max_aout 0

At the moment, there is no way to set a probablility threshold on pairwise alignments that is separate from the -probcut threshold.