The next part of the output contains the score list, ranked by Evalue. This is bounded by the key words ``Start_Scores'' and ``End_Scores''. Only the first 17 and last 6 scores are shown here:
# Start_Scores: ---------------------------------------------------- 1 450 56.95 2.05e-20 ANX3_RAT (P14669) Annexin III (Lipocort 2 439 55.40 9.61e-20 ANX3_MOUSE (O35639) Annexin III (Lipocort 3 392 48.78 7.26e-17 ANX3_HUMAN (P12429) Annexin III (Lipocort 4 255 29.48 1.75e-08 ANX5_MOUSE (P48036) Annexin V (Lipocortin 5 245 28.07 7.15e-08 ANX5_RAT (P14668) Annexin V (Lipocortin 6 245 28.07 7.18e-08 ANX5_HUMAN (P08758) Annexin V (Lipocortin 7 245 28.06 7.2e-08 ANX5_BOVIN (P81287) Annexin V (Lipocortin 8 247 27.78 9.52e-08 ANXB_HUMAN (P50995) Annexin A11 (Annexin 9 239 27.19 1.72e-07 ANX8_MOUSE (O35640) Annexin A8 (Annexin V 10 239 27.19 1.72e-07 ANX8_HUMAN (P13928) Annexin A8 (Annexin V 11 243 26.97 2.15e-07 ANX6_BOVIN (P79134) Annexin VI (Lipocorti 12 236 26.79 2.57e-07 ANX5_CHICK (P17153) Annexin V (Lipocortin 13 228 26.77 2.61e-07 ANX1_CHICK (Q92108) Annexin I (Lipocortin 14 240 26.44 3.63e-07 ANX6_HUMAN (P08133) Annexin VI (Lipocorti 15 237 26.38 3.88e-07 ANXB_RABIT (P33477) Annexin A11 (Annexin 16 237 26.38 3.88e-07 ANXB_MOUSE (P97384) Annexin A11 (Annexin 17 237 26.38 3.88e-07 ANXB_BOVIN (P27214) Annexin A11 (Annexin lines deleted here. 55 189 20.10 0.000207 ANX9_HUMAN (O76027) Annexin A9 (Annexin 3 56 187 19.91 0.000251 ANX4_FRAAN (P51074) Annexin-like protein 57 186 19.66 0.000319 AN11_COLLI (P14950) Annexin I, isoform P3 58 184 19.39 0.000419 ANX9_MOUSE (Q9JHQ0) Annexin A9 (Annexin 3 59 116 12.21 0.551 ANX2_PIG (P19620) Annexin II (Lipocorti 60 100 8.82 16.3 Y069_ARCFU (O30167) Hypothetical protein # End_Scores: ------------------------------------------------------
The columns are: 1: Rank, 2: Raw Score, 3: (Intermediary score - ignore, this will be deleted from a future release of SCANPS) 4: Evalue, 5: ID of database sequence, 6: Title of database sequence.
How many scores you see is controlled by the probcut, nptt, and max_nout command line options. nptt means ``numbers, print to threshold'' and is a toggle. For example, to print all results down to an Evalue of 100 you would add:
-aptt 1 -probcut 100
on the command line (the default is -aptt 1 -probcut 10). If you want to print all scores down to a rank, e.g. the top 50, rather than controlled by Evalue, then do the following:
-aptt 0 -max_nout 50
This is not recommended, unless you are trying to suppress a huge output. It is better to control output through the -probcut option.