# fasta36 -E 0.5 -F 0.3 -m 10 prot_mult.fasta protlib.fasta
FASTA searches a protein or DNA sequence data bank
 version 36.3.5c Dec, 2011(preload8)
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query: prot_mult.fasta
  1>>>random_s00 - 16 aa
Library: protlib.fasta
  1375680 residues in   250 sequences

Statistics: (shuffled [500]) MLE statistics: Lambda= 0.2698;  K=0.06486
 statistics sampled from 200 (200) to 500 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 1, E-join: 1 (0.996), E-opt: 0.2 (0.8), width:  16
 Scan time:  0.200
!! No sequences with E() < 0.5
>>><<<
  2>>>sp|Q9Y2H6|68-133 - 66 aa
Library: protlib.fasta
  1375680 residues in   250 sequences

Statistics: (shuffled [499]) MLE statistics: Lambda= 0.1336;  K=0.001973
 statistics sampled from 219 (219) to 499 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.986), E-opt: 0.2 (0.838), width:  16
 Scan time:  0.180

The best scores are:                                      opt bits E(250)
gi|291391832|ref|XP_002712264.1| PREDICTED: titin  (33406)  109 30.2    0.43

>>>sp|Q9Y2H6|68-133, 66 aa vs protlib.fasta library
; pg_name: fasta36
; pg_ver: 36.3.5c Dec, 2011(preload8)
; pg_argv:  fasta36 -E 0.5 -F 0.3 -m 10 prot_mult.fasta protlib.fasta; pg_name_alg: FASTA
; pg_ver_rel: 3.7 Nov 2010
; pg_matrix: BL50 (15:-5)
; pg_open-ext: -10 -2
; pg_ktup: 2
; pg_join_E(): 1 (0.986)
; pg_optcut_E(): 0.2 (0.838)
; mp_extrap: 60000 499
; mp_stats: (shuffled [499]) MLE statistics: Lambda= 0.1336;  K=0.001973
; mp_KS: -0.0000 (N=0) at  20
; mp_Algorithm: FASTA (3.7 Nov 2010) [optimized]
; mp_Parameters: BL50 matrix (15:-5), open/ext: -10/-2  ktup: 2, E-join: 1 (0.986), E-opt: 0.2 (0.838), width:  16
>>gi|291391832|ref|XP_002712264.1| PREDICTED: titin [Oryctolagus cuniculus]
; fa_frame: f
; fa_initn:  98
; fa_init1:  98
; fa_opt: 109
; fa_z-score: 95.1
; fa_bits: 30.2
; fa_expect:   0.43
; sw_score: 109
; sw_ident: 0.268
; sw_sim: 0.549
; sw_overlap: 71
>sp|Q9Y2H6|68 ..
; sq_len: 66
; sq_offset: 1
; sq_type: p
; al_start: 1
; al_stop: 66
; al_display_start: 1
------------------------------PNGSVPPIY-----VPPGYA
PQVIEDNGVRRVVVVPQAPEFHPGSHTVLHRSPHPPLPGFIPVPTMMPPP
P
>gi|291391832|ref|XP_002712264.1| ..
; sq_len: 33406
; sq_offset: 1
; sq_type: p
; al_start: 10705
; al_stop: 10775
; al_display_start: 10675
PVPEKKVPAVIAKKPEPPAVKVPEVPKEVVPEKKVPPAVPKKPEAPPAKV
PEAPKEVVPEKKIAVPKKPEVPPAKVPEVPKKPVIEEKPVIPVPKKVESP
PPEVYEEPEEVVPEEEPEEVVPEEEPIPVAEEEEPEAPPPAVPEEPKKIV
PEKKVPVIKKPEAPPPKEPEPEKKVVEKPK

>>><<<
  3>>>sp|Q9Y2H6|265-345 - 81 aa
Library: protlib.fasta
  1375680 residues in   250 sequences

Statistics: (shuffled [493]) MLE statistics: Lambda= 0.1643;  K=0.002885
 statistics sampled from 237 (237) to 493 sequences
Algorithm: FASTA (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -10/-2
 ktup: 2, E-join: 1 (0.989), E-opt: 0.2 (0.875), width:  16
 Scan time:  0.200

The best scores are:                                      opt bits E(250)
gi|260806189|ref|XP_002597967.1| hypothetical prot (23830)   91 30.5    0.32
gi|348553521|ref|XP_003462575.1| PREDICTED: recept (1899)   75 26.7    0.36
gi|348553523|ref|XP_003462576.1| PREDICTED: recept (1908)   75 26.7    0.36
gi|221124183|ref|XP_002154464.1| PREDICTED: simila ( 860)   69 25.3    0.43

>>>sp|Q9Y2H6|265-345, 81 aa vs protlib.fasta library
; pg_name: fasta36
; pg_ver: 36.3.5c Dec, 2011(preload8)
; pg_argv:  fasta36 -E 0.5 -F 0.3 -m 10 prot_mult.fasta protlib.fasta; pg_name_alg: FASTA
; pg_ver_rel: 3.7 Nov 2010
; pg_matrix: BL50 (15:-5)
; pg_open-ext: -10 -2
; pg_ktup: 2
; pg_join_E(): 1 (0.989)
; pg_optcut_E(): 0.2 (0.875)
; mp_extrap: 60000 493
; mp_stats: (shuffled [493]) MLE statistics: Lambda= 0.1643;  K=0.002885
; mp_KS: -0.0000 (N=0) at  20
; mp_Algorithm: FASTA (3.7 Nov 2010) [optimized]
; mp_Parameters: BL50 matrix (15:-5), open/ext: -10/-2  ktup: 2, E-join: 1 (0.989), E-opt: 0.2 (0.875), width:  16
>>gi|260806189|ref|XP_002597967.1| hypothetical protein BRAFLDRAFT_79792 [Branchiostoma floridae]
; fa_frame: f
; fa_initn: 220
; fa_init1:  62
; fa_opt:  92
; fa_z-score: 97.4
; fa_bits: 30.5
; fa_expect:   0.32
; sw_score: 92
; sw_ident: 0.316
; sw_sim: 0.608
; sw_overlap: 79
>sp|Q9Y2H6|26 ..
; sq_len: 81
; sq_offset: 1
; sq_type: p
; al_start: 2
; al_stop: 79
; al_display_start: 1
-----------------------------LLSNIVKPVASDIQARTVVLT
WSPPSSLINGETDESSVPELYGYEVLISSTGKDGKYKSVYVG-EETNITL
NDLKPAMDYHA
>gi|260806189|ref|XP_002597967.1| ..
; sq_len: 23830
; sq_offset: 1
; sq_type: p
; al_start: 22431
; al_stop: 22499
; al_display_start: 22401
KDDAGTYKVKVENENGYDECAITLHVIGKPVSNI-RPAASDISPHTLTLT
WDTP------EDDGGSLITSYVVEMFDVS---DGKWQTLTTTCRRPPYPV
KGLNPSATYRFRIRAENAYGLSDAGPLSDPILTKEPEQGRNDRSSDGKKT
DSSSSDSVAWRSTSMDSSSDADRVDRKIQA
>>gi|348553521|ref|XP_003462575.1| PREDICTED: receptor-type tyrosine-protein phosphatase F isoform 1 [Cavia porcellus]
; fa_frame: f
; fa_initn: 104
; fa_init1:  75
; fa_opt:  75
; fa_z-score: 96.6
; fa_bits: 26.7
; fa_expect:   0.36
; sw_score: 75
; sw_ident: 0.324
; sw_sim: 0.649
; sw_overlap: 37
>sp|Q9Y2H6|26 ..
; sq_len: 81
; sq_offset: 1
; sq_type: p
; al_start: 44
; al_stop: 80
; al_display_start: 14
QARTVVLTWSPPSSLINGETDESSVPELYGYEVLISSTGKDGKYKSVYVG
EETNITLNDLKPAMDYHA
>gi|348553521|ref|XP_003462575.1| ..
; sq_len: 1899
; sq_offset: 1
; sq_type: p
; al_start: 543
; al_stop: 579
; al_display_start: 513
AQPADFQAEAESDTRIQLSWLLPPQERIIKYELVYWAAEEEGQQRKVTFD
PTSSYTLEDLKPDTLYHFQLAARSDMGVGVFTPTIEARTAQSTPSAPPQK
VTCVSTGSTTVRVSWVPPPA
>>gi|348553523|ref|XP_003462576.1| PREDICTED: receptor-type tyrosine-protein phosphatase F isoform 2 [Cavia porcellus]
; fa_frame: f
; fa_initn: 104
; fa_init1:  75
; fa_opt:  75
; fa_z-score: 96.6
; fa_bits: 26.7
; fa_expect:   0.36
; sw_score: 75
; sw_ident: 0.324
; sw_sim: 0.649
; sw_overlap: 37
>sp|Q9Y2H6|26 ..
; sq_len: 81
; sq_offset: 1
; sq_type: p
; al_start: 44
; al_stop: 80
; al_display_start: 14
QARTVVLTWSPPSSLINGETDESSVPELYGYEVLISSTGKDGKYKSVYVG
EETNITLNDLKPAMDYHA
>gi|348553523|ref|XP_003462576.1| ..
; sq_len: 1908
; sq_offset: 1
; sq_type: p
; al_start: 543
; al_stop: 579
; al_display_start: 513
AQPADFQAEAESDTRIQLSWLLPPQERIIKYELVYWAAEEEGQQRKVTFD
PTSSYTLEDLKPDTLYHFQLAARSDMGVGVFTPTIEARTAQSTPSAPPQK
VTCVSTGSTTVRVSWVPPPA
>>gi|221124183|ref|XP_002154464.1| PREDICTED: similar to FAD104 [Hydra magnipapillata]
; fa_frame: f
; fa_initn:  85
; fa_init1:  66
; fa_opt:  70
; fa_z-score: 95.1
; fa_bits: 25.3
; fa_expect:   0.43
; sw_score: 70
; sw_ident: 0.271
; sw_sim: 0.586
; sw_overlap: 70
>sp|Q9Y2H6|26 ..
; sq_len: 81
; sq_offset: 1
; sq_type: p
; al_start: 10
; al_stop: 79
; al_display_start: 1
---------------------LLSNIVKPVASDIQARTVVLTWSPPSSLI
NGETDESSVPELYGYEVLISSTGKDGKYKSVYVGEETNITLNDLKPAMDY
HA
>gi|221124183|ref|XP_002154464.1| ..
; sq_len: 860
; sq_offset: 1
; sq_type: p
; al_start: 616
; al_stop: 673
; al_display_start: 586
QAVSEVGIGAFSQYVQFYTKELPPLAPTLSASSISYHSIKLKWGHQSS--
-----KKSI-----LNHTLQMQNKSGSFNTVYSGMDTSFTLSKLKELTPY
CFRIQSSNEAGEGQFSMPKVFYTKAQPPSHVKELKCQHVDISSIKLIWTP
VESIRPDDITKYTLQMQNVELGNNFNQVYN

>>><<<
>>>///

163 residues in 3 query   sequences
1375680 residues in 250 library sequences
 Tcomplib [36.3.5c Dec, 2011(preload8)] (4 proc in memory [0G])
 start: Tue May  8 01:06:58 2012 done: Tue May  8 01:06:58 2012
 Total Scan time:  0.580 Total Display time:  0.000

Function used was FASTA [36.3.5c Dec, 2011(preload8)]
