02336754147822f5aa61ba13277123b2cc629001 markd Thu May 20 08:38:55 2021 -0700 Moved pslMap, pslMapPostChain, pslRc, pslSwap to src/utils, as they do not have hg/lib dependencies. diff --git src/utils/pslMap/tests/input/gapBothProtMRna.blast src/utils/pslMap/tests/input/gapBothProtMRna.blast new file mode 100644 index 0000000..b65f045 --- /dev/null +++ src/utils/pslMap/tests/input/gapBothProtMRna.blast @@ -0,0 +1,218 @@ +TBLASTN 2.2.6 [Apr-09-2003] + + +Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, +Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), +"Gapped BLAST and PSI-BLAST: a new generation of protein database search +programs", Nucleic Acids Res. 25:3389-3402. + +Query= O14492 + (632 letters) + +Database: /cluster/bluearc/markd/snpProtein/kgMrna.fa + 37,452 sequences; 89,350,383 total letters + +Searching..................................................done + + Score E +Sequences producing significant alignments: (bits) Value + +AB000520 966 0.0 +AB037720 310 4e-84 +AL713760 310 4e-84 + +>AB000520 + Length = 2110 + + Score = 966 bits (2498), Expect = 0.0 + Identities = 489/611 (80%), Positives = 489/611 (80%) + Frame = +2 + +Query: 22 DWRQFCELHAQAAAVDFAHKFCRFLRDNPAYDTPDAGASFSRHFAANFLDVFGEEVRRVL 81 + DWRQFCELHAQAAAVDFAHKFCRFLRDNPAYDTPDAGASFSRHFAANFLDVFGEEVRRVL +Sbjct: 191 DWRQFCELHAQAAAVDFAHKFCRFLRDNPAYDTPDAGASFSRHFAANFLDVFGEEVRRVL 370 + +Query: 82 VAGPTTRGAAVSAEAMEPELADTSALKAASYGHSRSSEDVSTHAATKARVRKGFSLRNMS 141 + VAGPTTRGAAVSAEAMEPELADTSALKAASYGHSRSSEDVSTHAATKARVRKGFSLRNMS +Sbjct: 371 VAGPTTRGAAVSAEAMEPELADTSALKAASYGHSRSSEDVSTHAATKARVRKGFSLRNMS 550 + +Query: 142 LCVVDGVRDMWHRRASPEPDAAAAPRTAEPRDKWXXXXXXXXXXAAKVELVDIQREGALR 201 + LCVVDGVRDMWHRRASPEPDAAAAPRTAEPRDKW AAKVELVDIQREGALR +Sbjct: 551 LCVVDGVRDMWHRRASPEPDAAAAPRTAEPRDKWTRRLRLSRTLAAKVELVDIQREGALR 730 + +Query: 202 FMVXXXXXXXXXXXXQWQKCXXXXXXXXXXXXXXXXXXXPPKASRPKVSIPLSAIIEVRT 261 + FMV QWQKC PPKASRPKVSIPLSAIIEVRT +Sbjct: 731 FMVADDAAAGSGGSAQWQKCRLLLRRAVAEERFRLEFFVPPKASRPKVSIPLSAIIEVRT 910 + +Query: 262 TMPLEMPEKDNTFVLKVENGAEYILETIDSLQKHSWVADIQGCVDPGDSEEDTELSCTRG 321 + TMPLEMPEKDNTFVLKVENGAEYILETIDSLQKHSWVADIQGCVDPGDSEEDTELSCTRG +Sbjct: 911 TMPLEMPEKDNTFVLKVENGAEYILETIDSLQKHSWVADIQGCVDPGDSEEDTELSCTRG 1090 + +Query: 322 GCLASRVASCSCELLTDAVDLPRPPETTAVGAVVTAPHSRGRDAVRESLIHVPLETFLQT 381 + GCLASRVASCSCELLTDAVDLPRPPETTAVGAVVTAPHSRGRDAVRESLIHVPLETFLQT +Sbjct: 1091GCLASRVASCSCELLTDAVDLPRPPETTAVGAVVTAPHSRGRDAVRESLIHVPLETFLQT 1270 + +Query: 382 LESPGGSGSDSNNTGEQGAETDPEAEPELELSDYPWFHGTLSRVKAAQLVLAGGPRNHGL 441 + LESPGGSGSDSNNTGEQGAETDPEAEPELELSDYPWFHGTLSRVKAAQLVLAGGPRNHGL +Sbjct: 1271LESPGGSGSDSNNTGEQGAETDPEAEPELELSDYPWFHGTLSRVKAAQLVLAGGPRNHGL 1450 + +Query: 442 FVIRQSETRPGEYVLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVLDMLRHFHTHPIPL 501 + FVIRQSETRPGEYVLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVLDMLRHFHTHPIPL +Sbjct: 1451FVIRQSETRPGEYVLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVLDMLRHFHTHPIPL 1630 + +Query: 502 ESGGSADITLRSYVRAQDXXXXXXXXXXXXXXXXXCWSDSPGQHYFXXXXXXXXXXXXXX 561 + ESGGSADITLRSYVRAQD CWSDSPGQHYF +Sbjct: 1631ESGGSADITLRSYVRAQDPPPEPGPTPPAAPASPACWSDSPGQHYFSSLAAAACPPASPS 1810 + +Query: 562 XXXXXXXXXXXXXXXXXXXXXXRPVEGQLSARSRSNSXXXXXXXXXXXXXXXXXXXXXXX 621 + RPVEGQLSARSRSNS +Sbjct: 1811DAAGASSSSASSSSAASGPAPPRPVEGQLSARSRSNSAERLLEAVAATAAEEPPEAAPGR 1990 + +Query: 622 XXXXXNQYSFY 632 + NQYSFY +Sbjct: 1991ARAVENQYSFY 2023 + + +>AB037720 + Length = 6043 + + Score = 310 bits (795), Expect = 4e-84 + Identities = 223/601 (37%), Positives = 288/601 (47%), Gaps = 108/601 (17%) + Frame = +1 + +Query: 23 WRQFCELHAQAAAVDFAHKFCRFLRDNPAYDTPDAGASFSRHFAANFLDVFGEEVRRVL- 81 + WR+FCE HA+AAA+DFA +F +L +P Y P A A+FSR FA FL F EV R +Sbjct: 3367 WREFCESHARAAALDFARRFRLYLASHPQYAGPGAEAAFSRRFAELFLQHFEAEVARASG 3546 + +Query: 82 -----VAGPTTRGAAVSAEAMEPELADTSALKAASYGHSRSSEDV----------STHAA 126 + + P + GA +S + E A G SRSSED+ S+ + +Sbjct: 3547 SLSPPILAPLSPGAEISPHDLSLESCRVGG-PLAVLGPSRSSEDLAGPLPSSVSSSSTTS 3723 + +Query: 127 TKARVRKGFSLRNMSLCVVDGVRDMWHRRASPEPDAAAAPRTAE---------------- 170 + +K +++K FSLR++ V VR + R + +P ++A P +Sbjct: 3724 SKPKLKKRFSLRSVGRSVRGSVRGILQWRGTVDPPSSAGPLETSSGPPVLGGNSNSNSSG 3903 + +Query: 171 ---------------PRDKWXXXXXXXXXXAAKVELVD----IQREGALRFMVXXXXX-- 209 + P ++W L D +QRE L FM +Sbjct: 3904 GAGTVGRGLVSDGTSPGERWTHRFERLRLSRGGGALKDGAGMVQREELLSFMGAEEAAPD 4083 + +Query: 210 --------------XXXXXXXQWQKCXXXXXXXXXXXXXXXXXXX-PPKASRPKVSIPLS 254 + QWQKC PPKASRP++SIP S +Sbjct: 4084 PAGVGRGGGVAGPPSGGGGQPQWQKCRLLLRSEGEGGGGSRLEFFVPPKASRPRLSIPCS 4263 + +Query: 255 AIIEVRTTMPLEMPEKDNTFVLKVENGAEYILETIDSLQKHSWVADIQGCVDPGD----S 310 + +I +VRTT LEMP+++NTFV+KVE +EYI+ET+D+ +WV+DIQ C+ PG S +Sbjct: 4264 SITDVRTTTALEMPDRENTFVVKVEGPSEYIMETVDAQHVKAWVSDIQECLSPGPCPATS 4443 + +Query: 311 EEDTELSCTRGGCLASRVASCSCEL--LTDAVDLPR------PPETT------AVG---- 352 + L G +R + S EL L + LP P E+ A G +Sbjct: 4444 PRPMTLPLAPGTSFLTRENTDSLELSCLNHSESLPSQDLLLGPSESNDRLSQGAYGGLSD 4623 + +Query: 353 ----------AVVTAPHSRGRDAVRESLI-HVPLETFLQT-----LESPGGS-GSDSNNT 395 + A + A H + + L +P+E T L +P + T +Sbjct: 4624 RPSASISPSSASIAASHFDSMELLPPELPPRIPIEEGPPTGTVHPLSAPYPPLDTPETAT 4803 + +Query: 396 GEQGAETDPEA-EPELELSDYPWFHGTLSRVKAAQLVLAGGPRNHGLFVIRQSETRPGEY 454 + G + +PE E + LS YPWFHG LSR+KAAQLVL GG +HG+F++RQSETR GEY +Sbjct: 4804 GSFLFQGEPEGGEGDQPLSGYPWFHGMLSRLKAAQLVLTGGTGSHGVFLVRQSETRRGEY 4983 + +Query: 455 VLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVLDMLRHFHTHPIPLESGGSADITLRSY 514 + VLTFNFQGKAKHLRLSLN GQC VQHLWFQS+ DML HF HPIPLESGGS+D+ L SY +Sbjct: 4984 VLTFNFQGKAKHLRLSLNEEGQCRVQHLWFQSIFDMLEHFRVHPIPLESGGSSDVVLVSY 5163 + +Query: 515 V 515 + V +Sbjct: 5164 V 5166 + + +>AL713760 + Length = 4876 + + Score = 310 bits (795), Expect = 4e-84 + Identities = 222/601 (36%), Positives = 288/601 (47%), Gaps = 108/601 (17%) + Frame = +3 + +Query: 23 WRQFCELHAQAAAVDFAHKFCRFLRDNPAYDTPDAGASFSRHFAANFLDVFGEEVRRVL- 81 + WR+FCE HA+AAA+DFA +F +L +P Y P A A+FSR FA FL F EV R +Sbjct: 2178 WREFCESHARAAALDFARRFRLYLASHPQYAGPGAEAAFSRRFAELFLQHFEAEVARASG 2357 + +Query: 82 -----VAGPTTRGAAVSAEAMEPELADTSALKAASYGHSRSSEDV----------STHAA 126 + + P + GA +S + E A G SRSSED+ S+ + +Sbjct: 2358 SLSPPILAPLSPGAEISPHDLSLESCRVGG-PLAVLGPSRSSEDLAGPLPSSVSSSSTTS 2534 + +Query: 127 TKARVRKGFSLRNMSLCVVDGVRDMWHRRASPEPDAAAAPRTAE---------------- 170 + +K +++K FSLR++ V VR + R + +P ++A P +Sbjct: 2535 SKPKLKKRFSLRSVGRSVRGSVRGILQWRGTVDPPSSAGPLETSSGPPVLGGNSNSNSSG 2714 + +Query: 171 ---------------PRDKWXXXXXXXXXXAAKVELVD----IQREGALRFMVXXXXX-- 209 + P ++W L D +QRE L FM +Sbjct: 2715 GAGTVGRGLVSDGTSPGERWTHRFERLRLSRGGGALKDGAGMVQREELLSFMGAEEAAPD 2894 + +Query: 210 --------------XXXXXXXQWQKCXXXXXXXXXXXXXXXXXXX-PPKASRPKVSIPLS 254 + QWQKC PPKASRP++SIP S +Sbjct: 2895 PAGVGRGGGVAGPPSGGGGQPQWQKCRLLLRSEGEGGGGSRLEFFVPPKASRPRLSIPCS 3074 + +Query: 255 AIIEVRTTMPLEMPEKDNTFVLKVENGAEYILETIDSLQKHSWVADIQGCVDPGD----S 310 + +I +VRTT LEMP+++NTFV+KVE +EYI+ET+D+ +WV+DIQ C+ PG S +Sbjct: 3075 SITDVRTTTALEMPDRENTFVVKVEGPSEYIMETVDAQHVKAWVSDIQECLSPGPCPATS 3254 + +Query: 311 EEDTELSCTRGGCLASRVASCSCEL--LTDAVDLPR------PPETT------AVG---- 352 + L G +R + S EL L + LP P E+ A G +Sbjct: 3255 PRPMTLPLAPGTSFLTRENTDSLELSCLNHSESLPSQDLLLGPSESNDRLSQGAYGGLSD 3434 + +Query: 353 ----------AVVTAPHSRGRDAVRESLI-HVPLET-----FLQTLESPGGS-GSDSNNT 395 + A + A H + + L +P+E + L +P + T +Sbjct: 3435 RPSASISPSSASIAASHFDSMELLPPELPPRIPIEEGPPAGTVHPLSAPYPPLDTPETAT 3614 + +Query: 396 GEQGAETDPEA-EPELELSDYPWFHGTLSRVKAAQLVLAGGPRNHGLFVIRQSETRPGEY 454 + G + +PE E + LS YPWFHG LSR+KAAQLVL GG +HG+F++RQSETR GEY +Sbjct: 3615 GSFLFQGEPEGGEGDQPLSGYPWFHGMLSRLKAAQLVLTGGTGSHGVFLVRQSETRRGEY 3794 + +Query: 455 VLTFNFQGKAKHLRLSLNGHGQCHVQHLWFQSVLDMLRHFHTHPIPLESGGSADITLRSY 514 + VLTFNFQGKAKHLRLSLN GQC VQHLWFQS+ DML HF HPIPLESGGS+D+ L SY +Sbjct: 3795 VLTFNFQGKAKHLRLSLNEEGQCRVQHLWFQSIFDMLEHFRVHPIPLESGGSSDVVLVSY 3974 + +Query: 515 V 515 + V +Sbjct: 3975 V 3977 + + + Database: /cluster/bluearc/markd/snpProtein/kgMrna.fa + Posted date: Nov 13, 2003 9:35 AM + Number of letters in database: 89,350,383 + Number of sequences in database: 37,452 + +Lambda K H + 0.317 0.132 0.402 + +Gapped +Lambda K H + 0.267 0.0410 0.140 + + +Matrix: BLOSUM62 +Gap Penalties: Existence: 11, Extension: 1 +Number of Hits to DB: 65,697,381 +Number of Sequences: 37452 +Number of extensions: 1123227 +Number of successful extensions: 8055 +Number of sequences better than 10.0: 84 +Number of HSP's better than 10.0 without gapping: 3446 +Number of HSP's successfully gapped in prelim test: 592 +Number of HSP's that attempted gapping in prelim test: 4353 +Number of HSP's gapped (non-prelim): 4528 +length of query: 632 +length of database: 29,783,461 +effective HSP length: 113 +effective length of query: 519 +effective length of database: 25,551,385 +effective search space: 13261168815 +effective search space used: 13261168815 +frameshift window, decay const: 50, 0.1 +T: 13 +A: 40 +X1: 16 ( 7.3 bits) +X2: 38 (14.6 bits) +X3: 64 (24.7 bits) +S1: 41 (21.7 bits) +S2: 67 (30.4 bits)