22 March 2011

Blast Stylesheet : XML to HTML

I wrote a XSLT stylesheet for the following question on Biostar: I'd like to create an HTML file (from the XML file and XSL stylesheet) similar to what It can be achieved when we performed a BLAST search on the NCBI server.

The stylesheet I wrote is available on github at: https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/ncbi/blast2html.xsl. (see also my previous post blast2svg )

Usage:

xsltproc --novalid blast2html.xsl blast.xml > blast.html

Example:

Here is a XML output of blast:
<BlastOutput>
<BlastOutput_program>blastp</BlastOutput_program>
<BlastOutput_version>BLASTP 2.2.25+</BlastOutput_version>
<BlastOutput_reference>Alejandro A. Sch&auml;ffer, L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001), "Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements", Nucleic Acids Res. 29:2994-3005.</BlastOutput_reference>
<BlastOutput_db>N/A</BlastOutput_db>
<BlastOutput_query-ID>gi|187956781|gb|AAI40897.1|</BlastOutput_query-ID>
<BlastOutput_query-def>EIF4G1 protein [Homo sapiens]</BlastOutput_query-def>
<BlastOutput_query-len>1606</BlastOutput_query-len>
<BlastOutput_param>
<Parameters>
<Parameters_matrix>BLOSUM62</Parameters_matrix>
<Parameters_expect>10</Parameters_expect>
<Parameters_gap-open>11</Parameters_gap-open>
<Parameters_gap-extend>1</Parameters_gap-extend>
<Parameters_filter>F</Parameters_filter>
</Parameters>
</BlastOutput_param>
<BlastOutput_iterations>
<Iteration>
<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_query-ID>gi|187956781|gb|AAI40897.1|</Iteration_query-ID>
<Iteration_query-def>EIF4G1 protein [Homo sapiens]</Iteration_query-def>
<Iteration_query-len>1606</Iteration_query-len>
<Iteration_hits>
<Hit>
<Hit_num>1</Hit_num>
<Hit_id>gi|293340930|ref|XP_002724789.1|</Hit_id>
<Hit_def>PREDICTED: eukaryotic translation initiation factor 4 gamma, 1 isoform 2 [Rattus norvegicus] >gi|293352298|ref|XP_002727969.1| PREDICTED: eukaryotic translation initiation factor 4, gamma 1 isoform 1 [Rattus norvegicus]</Hit_def>
<Hit_accession>XP_002727969</Hit_accession>
<Hit_len>1584</Hit_len>
<Hit_hsps>
<Hsp>
<Hsp_num>1</Hsp_num>
<Hsp_bit-score>2715.64</Hsp_bit-score>
<Hsp_score>7038</Hsp_score>
<Hsp_evalue>0</Hsp_evalue>
<Hsp_query-from>1</Hsp_query-from>
<Hsp_query-to>1606</Hsp_query-to>
<Hsp_hit-from>1</Hsp_hit-from>
<Hsp_hit-to>1584</Hsp_hit-to>
<Hsp_query-frame>0</Hsp_query-frame>
<Hsp_hit-frame>0</Hsp_hit-frame>
<Hsp_identity>1450</Hsp_identity>
<Hsp_positive>1450</Hsp_positive>
<Hsp_gaps>36</Hsp_gaps>
<Hsp_align-len>1613</Hsp_align-len>
<Hsp_qseq>MNKAPQSTGPPPAPSPGLPQPAFPPGQTAPVVFSTPQATQMNTPSQPRQGGFRSLQHFYPSRAQPPSSAASRVQSAAPARPGPAAHVYPAGSQVMMIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPTPPQTGGGLEPQANGETPQVAVIVRPDDRSQGAIIADRPGLPGPEHSP-SESQPSSPSPTPSPSPVLEPGSEPNLAVLSIPGDTMTT--IQMSVEESTPISRETGEPYRLSPEPTPLAEPILEVEVTLSKPVPESEFSSSPLQAPTPLASHTVEIHEPNGMVPSEDLEPEVESSPELAPPP--ACPSESPVPIAPTAQPEELLNGAPSPPAVDLSPVSEPEEQAKEV-TASMAPPTIPSATPATAPSATSPAQEEEMEEEEEEEEGEAGEAGEAESEKGGEELLPPESTPIPANLSQNLEAAAATQVAVSVPKRRRKIKELNKKEAVGDLLDAFKEANPAVPEVENQPPAGSNPGPESEGSGVPPRPEEADETWDSKEDKIHNAENIQPGEQKYEYKSDQWKPLNLEEKKRYDREFLLGFQFIFASMQKPEGLPHISDVVLDKANKTPLRPLDPTRLQGINCGPDFTPSFANLGRTTLSTRGPPRGGPGGELPRGPAGLGPRRSQQGPRKEPRKIIATVLMTEDIKLNKAEKAWKPSSKRTAADKDRGEEDADGSKTQDLFRRVRSILNKLTPQMFQQLMKQVTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCLMALKVPTTEKPTVTVNFRKLLLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLKEELEEARDIARRRSLGNIKFIGELFKLKMLTEAIMHDCVVKLLKNHDEESLECLCRLLTTIGKDLDFEKAKPRMDQYFNQMEKIIKEKKTSSRIRFMLQDVLDLRGSNWVPRRGDQGPKTIDQIHKEAEMEEHREHIKVQQLMAKGSDKRRGGPPGPPISRGLPLVDDGGWNTVPISKGSRPIDTSRLTKITKPGSIDSNNQLFAPGGRLSWGKGSSGGSGAKPSDAASEAARPATSTLNRFSALQQAVPTESTDNRRVVQRSSLSRERGEKAGDRGDRLERSERGGDRGDRLDRARTPATKRSFSKEVEERSRERPSQPEGLRKAASLTEDRDRGRDAVKREAALPPVSPLKAALSEEELEKKSKAIIEEYLHLNDMKEAVQCVQELASPSLLFIFVRHGVESTLERSAIAREHMGQLLHQLLCAGHLSTAQYYQGLYEILELAEDMEIDIPHVWLYLAELVTPILQEGGVPMGELFREITKPLRPLGKAASLLLEILGLLCKSMGPKKVGTLWREAGLSWKEFLPEGQDIGAFVAEQKVEYTLGEESEAPGQRALPSEELNRQLEKLLKEGSSNQRVFDWIEANLSEQQIVSNTLVRALMTAVCYSAIIFETPLRVDVAVLKARAKLLQKYLCDEQKELQALYALQALVVTLEQPPNLLRMFFDALYDEDVVKEDAFYSWESSKDPAEQQGKGVALKSVTAFFKWLREAE-EESDHN</Hsp_qseq>
<Hsp_hseq>MNKAPQPTGPPPARSPGLPQPAFPPGQTAPVVFSTPQATQMNTPSQPRQ-------HFYPSRAQPPSSAASRVQSAAPARPGPAPHVYPAGSQVMMIPSQISYSASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQSVQQFPASVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPTPPQTGGSLEPQPNGESPQVAVIIRPDDRSQGAAIGGRPGLPGPEHSPGTESQPSSPSPTPSPPPILEPGSESNLGVLSIPGDTMTTGMIPISVEESTPISCESGEPYCLSPEPT-LAEPILEVEVTLSKPIPESEFSSSPLQVSTSLVPHRAETHEPNGVIPSEDLEPEVESSTEPAPPPLSACASESLVPIAPTAQPEELLNGAPSPPAVDLSPVSEPEEQAKEVPSAALA--SIVSPTPPVAPSDTSAAQEEEIEED-------EDEDGEAESEKGGEDL-PLDSTPVPAQLSQNLEVAAAPQVAVSVPKRRRKIKELNKKEAVGDLLDAFKEVDPAVPEVENQPPTGSNPSPESEGSAALPQPEEAEETWDSKEDKIHNAENIQPGEQKYEYKSDQWKPLNLEEKKRYDREFLLGFQFIFASMQKPEGLPHITDVVLDKANKTPLRSLDPSRLPGINCGPDFTPSFANLGRPTLSSRGPPRGGPGGELPRGPAGLGPRRSQQGPRKETRKIISSVIMTEDIKLNKAEKAWKPSSKRTAADKDRGEEDADGSKTQDLFRRVRSILNKLTPQMFQQLMKQVTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCLMALKVPTTEKPTVTVNFRKLLLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLKEELEEARDIARRRSLGNIKFIGELFKLKMLTEAIMHDCVVKLLKNHDEESLECLCRLLTTIGKDLDFAKAKPRMDQYFNQMEKIIKEKKTSSRIRFMLQDVLDLRQSNWVPRRGDQGPKTIDQIHKEAEMEEHREHIKVQQLMAKGGDKRRGGPPGPP-------VNDGGWNTVPISKGSRPIDTSRLTKITKPGSIDSNNQLFAPGGRLSWGKGSSGGSGAKPSDTASEATRPA--TLNRFSALQQTLPVENTDNRRVVQRSSLSRERGEKAGDRGDRLERSERGGDRGDRLDRARTPATKRSFSKEVEERSRERPSQPEGLRKAASLTE--DRGRDPVKREATLPPVSPPKAALAVDEVERKSKAIIEEYLHLNDMKEAVQCVQELASPSLLFIFVRLGIESTLERSTIAREHMGRLLHQLLCAGHLSTAQYYQGLYETLELAEDMEIDIPHVWLYLAELITPILQEDGVPMGELFREITKPLRPMGKATSLLLEILGLLCKSMGPKKVGMLWREAGLSWREFLAEGQDVGSFVAEKKVEYTLGEESEAPGQRALAFEELRRQLEKLLKDGGSNQRVFDWIEANLNEQQIASNTLVRALMTTVCYSAIIFETPLRVDVQVLKVRARLLQKYLSDEQKELQALYALQALVVTLEQPANLLRMFFDALYDEDVVKEDAFYSWESSKDPAEQQGKGVALKSVTAFFNWLREAEDEESDHN</Hsp_hseq>
<Hsp_midline>MNKAPQ TGPPPA SPGLPQPAFPPGQTAPVVFSTPQATQMNTPSQPRQ HFYPSRAQPPSSAASRVQSAAPARPGPA HVYPAGSQVMMIPSQISY ASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQ VQQFP VAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPTPPQTGG LEPQ NGE PQVAVI RPDDRSQGA I RPGLPGPEHSP ESQPSSPSPTPSP P LEPGSE NL VLSIPGDTMTT I SVEESTPIS E GEPY LSPEPT LAEPILEVEVTLSKP PESEFSSSPLQ T L H E HEPNG PSEDLEPEVESS E APPP AC SES VPIAPTAQPEELLNGAPSPPAVDLSPVSEPEEQAKEV A A I S TP APS TS AQEEE EE E GEAESEKGGE L P STP PA LSQNLE AAA QVAVSVPKRRRKIKELNKKEAVGDLLDAFKE PAVPEVENQPP GSNP PESEGS P PEEA ETWDSKEDKIHNAENIQPGEQKYEYKSDQWKPLNLEEKKRYDREFLLGFQFIFASMQKPEGLPHI DVVLDKANKTPLR LDP RL GINCGPDFTPSFANLGR TLS RGPPRGGPGGELPRGPAGLGPRRSQQGPRKE RKII V MTEDIKLNKAEKAWKPSSKRTAADKDRGEEDADGSKTQDLFRRVRSILNKLTPQMFQQLMKQVTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCLMALKVPTTEKPTVTVNFRKLLLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLKEELEEARDIARRRSLGNIKFIGELFKLKMLTEAIMHDCVVKLLKNHDEESLECLCRLLTTIGKDLDF KAKPRMDQYFNQMEKIIKEKKTSSRIRFMLQDVLDLR SNWVPRRGDQGPKTIDQIHKEAEMEEHREHIKVQQLMAKG DKRRGGPPGPP V DGGWNTVPISKGSRPIDTSRLTKITKPGSIDSNNQLFAPGGRLSWGKGSSGGSGAKPSD ASEA RPA TLNRFSALQQ P E TDNRRVVQRSSLSRERGEKAGDRGDRLERSERGGDRGDRLDRARTPATKRSFSKEVEERSRERPSQPEGLRKAASLTE DRGRD VKREA LPPVSP KAAL E E KSKAIIEEYLHLNDMKEAVQCVQELASPSLLFIFVR G ESTLERS IAREHMG LLHQLLCAGHLSTAQYYQGLYE LELAEDMEIDIPHVWLYLAEL TPILQE GVPMGELFREITKPLRP GKA SLLLEILGLLCKSMGPKKVG LWREAGLSW EFL EGQD G FVAE KVEYTLGEESEAPGQRAL EEL RQLEKLLK G SNQRVFDWIEANL EQQI SNTLVRALMT VCYSAIIFETPLRVDV VLK RA LLQKYL DEQKELQALYALQALVVTLEQP NLLRMFFDALYDEDVVKEDAFYSWESSKDPAEQQGKGVALKSVTAFF WLREAE EESDHN</Hsp_midline>
</Hsp>
</Hit_hsps>
</Hit>
</Iteration_hits>
<Iteration_stat>
<Statistics>
<Statistics_db-num>0</Statistics_db-num>
<Statistics_db-len>0</Statistics_db-len>
<Statistics_hsp-len>0</Statistics_hsp-len>
<Statistics_eff-space>0</Statistics_eff-space>
<Statistics_kappa>-1</Statistics_kappa>
<Statistics_lambda>-1</Statistics_lambda>
<Statistics_entropy>-1</Statistics_entropy>
</Statistics>
</Iteration_stat>
</Iteration>
</BlastOutput_iterations>
</BlastOutput>

After processing:

(...)

Descriptions

AccessionDefe-value
XP_002727969PREDICTED: eukaryotic translation initiation factor 4 gamma, 1 isoform 2 [Rattus norvegicus] >gi|293352298|ref|XP_002727969.1| PREDICTED: eukaryotic translation initiation factor 4, gamma 1 isoform 1 [Rattus norvegicus]0
(...)

Alignments

>gi|293340930|ref|XP_002724789.1||XP_002727969|PREDICTED: eukaryotic translation initiation factor 4 gamma, 1 isoform 2 [Rattus norvegicus] >gi|293352298|ref|XP_002727969.1| PREDICTED: eukaryotic translation initiation factor 4, gamma 1 isoform 1 [Rattus norvegicus]
Length=1584
Score = 2715.64 bits (7038), Expect = 0
Identities = 1450/1613 (89.8946063236206%), Gaps = 36/1613 (2.231866088034718%)
Strand = Plus/Plus

Query 1        MNKAPQSTGPPPAPSPGLPQPAFPPGQTAPVVFSTPQATQMNTPSQPRQGGFRSLQHFYP 60
               MNKAPQ TGPPPA SPGLPQPAFPPGQTAPVVFSTPQATQMNTPSQPRQ       HFYP
Sbjct 1        MNKAPQPTGPPPARSPGLPQPAFPPGQTAPVVFSTPQATQMNTPSQPRQ-------HFYP 53

Query 61       SRAQPPSSAASRVQSAAPARPGPAAHVYPAGSQVMMIPSQISYPASQGAYYIPGQGRSTY 120
               SRAQPPSSAASRVQSAAPARPGPA HVYPAGSQVMMIPSQISY ASQGAYYIPGQGRSTY
Sbjct 54       SRAQPPSSAASRVQSAAPARPGPAPHVYPAGSQVMMIPSQISYSASQGAYYIPGQGRSTY 113

Query 121      VVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAP 180
               VVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQ VQQFP  VAPAPVLMNQPPQIAP
Sbjct 114      VVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQSVQQFPASVAPAPVLMNQPPQIAP 173

Query 181      KRERKTIRIRDPNQGGKDITEEIMSGARTASTPTPPQTGGGLEPQANGETPQVAVIVRPD 240
               KRERKTIRIRDPNQGGKDITEEIMSGARTASTPTPPQTGG LEPQ NGE PQVAVI RPD
Sbjct 174      KRERKTIRIRDPNQGGKDITEEIMSGARTASTPTPPQTGGSLEPQPNGESPQVAVIIRPD 233

Query 241      DRSQGAIIADRPGLPGPEHSP-SESQPSSPSPTPSPSPVLEPGSEPNLAVLSIPGDTMTT 299
               DRSQGA I  RPGLPGPEHSP  ESQPSSPSPTPSP P LEPGSE NL VLSIPGDTMTT
Sbjct 234      DRSQGAAIGGRPGLPGPEHSPGTESQPSSPSPTPSPPPILEPGSESNLGVLSIPGDTMTT 293

Query 300      --IQMSVEESTPISRETGEPYRLSPEPTPLAEPILEVEVTLSKPVPESEFSSSPLQAPTP 357
                 I  SVEESTPIS E GEPY LSPEPT LAEPILEVEVTLSKP PESEFSSSPLQ  T 
Sbjct 294      GMIPISVEESTPISCESGEPYCLSPEPT-LAEPILEVEVTLSKPIPESEFSSSPLQVSTS 352

Query 358      LASHTVEIHEPNGMVPSEDLEPEVESSPELAPPP--ACPSESPVPIAPTAQPEELLNGAP 415
               L  H  E HEPNG  PSEDLEPEVESS E APPP  AC SES VPIAPTAQPEELLNGAP
Sbjct 353      LVPHRAETHEPNGVIPSEDLEPEVESSTEPAPPPLSACASESLVPIAPTAQPEELLNGAP 412

Query 416      SPPAVDLSPVSEPEEQAKEV-TASMAPPTIPSATPATAPSATSPAQEEEMEEEEEEEEGE 474
               SPPAVDLSPVSEPEEQAKEV  A  A   I S TP  APS TS AQEEE EE        
Sbjct 413      SPPAVDLSPVSEPEEQAKEVPSAALA--SIVSPTPPVAPSDTSAAQEEEIEED------- 463

Query 475      AGEAGEAESEKGGEELLPPESTPIPANLSQNLEAAAATQVAVSVPKRRRKIKELNKKEAV 534
                 E GEAESEKGGE L P  STP PA LSQNLE AAA QVAVSVPKRRRKIKELNKKEAV
Sbjct 464      EDEDGEAESEKGGEDL-PLDSTPVPAQLSQNLEVAAAPQVAVSVPKRRRKIKELNKKEAV 522

Query 535      GDLLDAFKEANPAVPEVENQPPAGSNPGPESEGSGVPPRPEEADETWDSKEDKIHNAENI 594
               GDLLDAFKE  PAVPEVENQPP GSNP PESEGS   P PEEA ETWDSKEDKIHNAENI
Sbjct 523      GDLLDAFKEVDPAVPEVENQPPTGSNPSPESEGSAALPQPEEAEETWDSKEDKIHNAENI 582

Query 595      QPGEQKYEYKSDQWKPLNLEEKKRYDREFLLGFQFIFASMQKPEGLPHISDVVLDKANKT 654
               QPGEQKYEYKSDQWKPLNLEEKKRYDREFLLGFQFIFASMQKPEGLPHI DVVLDKANKT
Sbjct 583      QPGEQKYEYKSDQWKPLNLEEKKRYDREFLLGFQFIFASMQKPEGLPHITDVVLDKANKT 642

Query 655      PLRPLDPTRLQGINCGPDFTPSFANLGRTTLSTRGPPRGGPGGELPRGPAGLGPRRSQQG 714
               PLR LDP RL GINCGPDFTPSFANLGR TLS RGPPRGGPGGELPRGPAGLGPRRSQQG
Sbjct 643      PLRSLDPSRLPGINCGPDFTPSFANLGRPTLSSRGPPRGGPGGELPRGPAGLGPRRSQQG 702

Query 715      PRKEPRKIIATVLMTEDIKLNKAEKAWKPSSKRTAADKDRGEEDADGSKTQDLFRRVRSI 774
               PRKE RKII  V MTEDIKLNKAEKAWKPSSKRTAADKDRGEEDADGSKTQDLFRRVRSI
Sbjct 703      PRKETRKIISSVIMTEDIKLNKAEKAWKPSSKRTAADKDRGEEDADGSKTQDLFRRVRSI 762

Query 775      LNKLTPQMFQQLMKQVTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCLMALKV 834
               LNKLTPQMFQQLMKQVTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCLMALKV
Sbjct 763      LNKLTPQMFQQLMKQVTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCLMALKV 822

Query 835      PTTEKPTVTVNFRKLLLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLKEELEEA 894
               PTTEKPTVTVNFRKLLLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLKEELEEA
Sbjct 823      PTTEKPTVTVNFRKLLLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLKEELEEA 882

Query 895      RDIARRRSLGNIKFIGELFKLKMLTEAIMHDCVVKLLKNHDEESLECLCRLLTTIGKDLD 954
               RDIARRRSLGNIKFIGELFKLKMLTEAIMHDCVVKLLKNHDEESLECLCRLLTTIGKDLD
Sbjct 883      RDIARRRSLGNIKFIGELFKLKMLTEAIMHDCVVKLLKNHDEESLECLCRLLTTIGKDLD 942

Query 955      FEKAKPRMDQYFNQMEKIIKEKKTSSRIRFMLQDVLDLRGSNWVPRRGDQGPKTIDQIHK 1014
               F KAKPRMDQYFNQMEKIIKEKKTSSRIRFMLQDVLDLR SNWVPRRGDQGPKTIDQIHK
Sbjct 943      FAKAKPRMDQYFNQMEKIIKEKKTSSRIRFMLQDVLDLRQSNWVPRRGDQGPKTIDQIHK 1002

Query 1015     EAEMEEHREHIKVQQLMAKGSDKRRGGPPGPPISRGLPLVDDGGWNTVPISKGSRPIDTS 1074
               EAEMEEHREHIKVQQLMAKG DKRRGGPPGPP       V DGGWNTVPISKGSRPIDTS
Sbjct 1003     EAEMEEHREHIKVQQLMAKGGDKRRGGPPGPP-------VNDGGWNTVPISKGSRPIDTS 1055

Query 1075     RLTKITKPGSIDSNNQLFAPGGRLSWGKGSSGGSGAKPSDAASEAARPATSTLNRFSALQ 1134
               RLTKITKPGSIDSNNQLFAPGGRLSWGKGSSGGSGAKPSD ASEA RPA  TLNRFSALQ
Sbjct 1056     RLTKITKPGSIDSNNQLFAPGGRLSWGKGSSGGSGAKPSDTASEATRPA--TLNRFSALQ 1113

Query 1135     QAVPTESTDNRRVVQRSSLSRERGEKAGDRGDRLERSERGGDRGDRLDRARTPATKRSFS 1194
               Q  P E TDNRRVVQRSSLSRERGEKAGDRGDRLERSERGGDRGDRLDRARTPATKRSFS
Sbjct 1114     QTLPVENTDNRRVVQRSSLSRERGEKAGDRGDRLERSERGGDRGDRLDRARTPATKRSFS 1173

Query 1195     KEVEERSRERPSQPEGLRKAASLTEDRDRGRDAVKREAALPPVSPLKAALSEEELEKKSK 1254
               KEVEERSRERPSQPEGLRKAASLTE  DRGRD VKREA LPPVSP KAAL   E E KSK
Sbjct 1174     KEVEERSRERPSQPEGLRKAASLTE--DRGRDPVKREATLPPVSPPKAALAVDEVERKSK 1231

Query 1255     AIIEEYLHLNDMKEAVQCVQELASPSLLFIFVRHGVESTLERSAIAREHMGQLLHQLLCA 1314
               AIIEEYLHLNDMKEAVQCVQELASPSLLFIFVR G ESTLERS IAREHMG LLHQLLCA
Sbjct 1232     AIIEEYLHLNDMKEAVQCVQELASPSLLFIFVRLGIESTLERSTIAREHMGRLLHQLLCA 1291

Query 1315     GHLSTAQYYQGLYEILELAEDMEIDIPHVWLYLAELVTPILQEGGVPMGELFREITKPLR 1374
               GHLSTAQYYQGLYE LELAEDMEIDIPHVWLYLAEL TPILQE GVPMGELFREITKPLR
Sbjct 1292     GHLSTAQYYQGLYETLELAEDMEIDIPHVWLYLAELITPILQEDGVPMGELFREITKPLR 1351

Query 1375     PLGKAASLLLEILGLLCKSMGPKKVGTLWREAGLSWKEFLPEGQDIGAFVAEQKVEYTLG 1434
               P GKA SLLLEILGLLCKSMGPKKVG LWREAGLSW EFL EGQD G FVAE KVEYTLG
Sbjct 1352     PMGKATSLLLEILGLLCKSMGPKKVGMLWREAGLSWREFLAEGQDVGSFVAEKKVEYTLG 1411

Query 1435     EESEAPGQRALPSEELNRQLEKLLKEGSSNQRVFDWIEANLSEQQIVSNTLVRALMTAVC 1494
               EESEAPGQRAL  EEL RQLEKLLK G SNQRVFDWIEANL EQQI SNTLVRALMT VC
Sbjct 1412     EESEAPGQRALAFEELRRQLEKLLKDGGSNQRVFDWIEANLNEQQIASNTLVRALMTTVC 1471

Query 1495     YSAIIFETPLRVDVAVLKARAKLLQKYLCDEQKELQALYALQALVVTLEQPPNLLRMFFD 1554
               YSAIIFETPLRVDV VLK RA LLQKYL DEQKELQALYALQALVVTLEQP NLLRMFFD
Sbjct 1472     YSAIIFETPLRVDVQVLKVRARLLQKYLSDEQKELQALYALQALVVTLEQPANLLRMFFD 1531

Query 1555     ALYDEDVVKEDAFYSWESSKDPAEQQGKGVALKSVTAFFKWLREAE-EESDHN 1606
               ALYDEDVVKEDAFYSWESSKDPAEQQGKGVALKSVTAFF WLREAE EESDHN
Sbjct 1532     ALYDEDVVKEDAFYSWESSKDPAEQQGKGVALKSVTAFFNWLREAEDEESDHN 1584



That's it,

Pierre

Publié par Pierre Lindenbaum at 9:45 PM

Libellés : , , , ,

2 comments:

Anonymous said...

Thanks for the post!!!

Wednesday, 06 April, 2011
KHoegenauer said...

Thanks! This (or more specifically, the Blast2tsv version) is exactly what I need... almost...
It's designed for a single query sequence, but I'd like to modify it to work with multiple iterations (result of running BLAST with fasta file containing multiple sequences), then annotate the iteration definitions and lengths.
I understand I'll need to add another for-each loop, modify the XPath pointers (...XPaths...?), and set/call variables for the two new fields.
But, I am new to XSLT and am screwing up somewhere; most likely in the match/select statements.
Any suggestions?

[Also noticed that "Hit_def" and "Hit_len" are "Hit-def" and "Hit-len" in the TSV version, causing a few minor holes in the output.]

Thanks again for the great code/help

Friday, 29 June, 2012

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