Alignment iterator for the FASTA tool’s pairwise alignment output.

This is for reading the pairwise alignments output by Bill Pearson’s FASTA program when called with the -m 10 command line option for machine readable output. For more details about the FASTA tools, see the website http://fasta.bioch.virginia.edu/ and the paper:

 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

This class is intended to be used via the Bio.AlignIO.parse() function by specifying the format as “fasta-m10” as shown in the following code::

from Bio import AlignIO
handle = ...
for a in AlignIO.parse(handle, "fasta-m10"):
  assert len(a) == 2, "Should be pairwise!"
  print("Alignment length %i" % a.get_alignment_length())
  for record in a:
    print("%s %s %s" % (record.seq, record.name, record.id))

Note that this is not a full blown parser for all the information in the FASTA output - for example, most of the header and all of the footer is ignored. Also, the alignments are not batched according to the input queries.

Also note that there can be up to about 30 letters of flanking region included in the raw FASTA output as contextual information. This is NOT part of the alignment itself, and is not included in the resulting MultipleSeqAlignment objects returned.

Extract alignment region (PRIVATE).

Helper function for the main parsing code.

To get the actual pairwise alignment sequences, we must first translate the un-gapped sequence based coordinates into positions in the gapped sequence (which may have a flanking region shown using leading - characters). To date, I have never seen any trailing flanking region shown in the m10 file, but the following code should also cope with that.

Note that this code seems to work fine even when the “sq_offset” entries are prsent as a result of using the -X command line option.

FASTA searches a protein or DNA sequence data bank version 34.26 January 12, 2007 Please cite: W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query library NC_002127.faa vs NC_009649.faa library searching NC_009649.faa library

1>>>gi|10955263|ref|NP_052604.1| plasmid mobilization [Escherichia coli O157:H7 s 107 aa - 107 aa vs NC_009649.faa library

45119 residues in 180 sequences Expectation_n fit: rho(ln(x))= 6.9146+/-0.0249; mu= -5.7948+/- 1.273 mean_var=53.6859+/-13.609, 0’s: 0 Z-trim: 1 B-trim: 9 in 1/25 Lambda= 0.175043

FASTA (3.5 Sept 2006) function [optimized, BL50 matrix (15:-5)] ktup: 2 join: 36, opt: 24, open/ext: -10/-2, width: 16 Scan time: 0.000 The best scores are: opt bits E(180) gi|152973457|ref|YP_001338508.1| ATPase with chape ( 931) 71 24.9 0.58 gi|152973588|ref|YP_001338639.1| F pilus assembly ( 459) 63 23.1 0.99

>>>gi|10955263|ref|NP_052604.1|, 107 aa vs NC_009649.faa library ; pg_name: /opt/fasta/fasta34 ; pg_ver: 34.26 ; pg_argv: /opt/fasta/fasta34 -Q -H -E 1 -m 10 NC_002127.faa NC_009649.faa ; pg_name: FASTA ; pg_ver: 3.5 Sept 2006 ; pg_matrix: BL50 (15:-5) ; pg_open-ext: -10 -2 ; pg_ktup: 2 ; pg_optcut: 24 ; pg_cgap: 36 ; mp_extrap: 60000 180 ; mp_stats: Expectation_n fit: rho(ln(x))= 6.9146+/-0.0249; mu= -5.7948+/- 1.273 mean_var=53.6859+/-13.609, 0’s: 0 Z-trim: 1 B-trim: 9 in 1/25 Lambda= 0.175043 ; mp_KS: -0.0000 (N=0) at 8159228 >>gi|152973457|ref|YP_001338508.1| ATPase with chaperone activity, ATP-binding subunit [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] ; fa_frame: f ; fa_initn: 65 ; fa_init1: 43 ; fa_opt: 71 ; fa_z-score: 90.3 ; fa_bits: 24.9 ; fa_expect: 0.58 ; sw_score: 71 ; sw_ident: 0.250 ; sw_sim: 0.574 ; sw_overlap: 108 >gi|10955263| .. ; sq_len: 107 ; sq_offset: 1 ; sq_type: p ; al_start: 5 ; al_stop: 103 ; al_display_start: 1 —————————————MTKRSGSNT-RRRAISRPVRLTAE ED—-QEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVM——- RLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD >gi|152973457|ref|YP_001338508.1| .. ; sq_len: 931 ; sq_type: p ; al_start: 96 ; al_stop: 195 ; al_display_start: 66 SDFFRIGDDATPVAADTDDVVDASFGEPAAAGSGAPRRRGSGLASRISEQ SEALLQEAAKHAAEFGRS———EVDTEHLLLALADSDVVKTILGQFKI KVDDLKRQIESEAKR-GDKPF-EGEIGVSPRVKDALSRAFVASNELGHSY VGPEHFLIGLAEEGEGLAANLLRRYGLTPQ >>gi|152973588|ref|YP_001338639.1| F pilus assembly protein [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] ; fa_frame: f ; fa_initn: 33 ; fa_init1: 33 ; fa_opt: 63 ; fa_z-score: 86.1 ; fa_bits: 23.1 ; fa_expect: 0.99 ; sw_score: 63 ; sw_ident: 0.266 ; sw_sim: 0.656 ; sw_overlap: 64 >gi|10955263| .. ; sq_len: 107 ; sq_offset: 1 ; sq_type: p ; al_start: 32 ; al_stop: 94 ; al_display_start: 2 TKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKK VNSLTDDRVLKEV-MRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRAL LSRLMAD >gi|152973588|ref|YP_001338639.1| .. ; sq_len: 459 ; sq_type: p ; al_start: 191 ; al_stop: 248 ; al_display_start: 161 VGGLFPRTQVAQQKVCQDIAGESNIFSDWAASRQGCTVGG—KMDSVQDK ASDKDKERVMKNINIMWNALSKNRLFDG——NKELKEFIMTLTGTLIFG ENSEITPLPARTTDQDLIRAMMEGGTAKIYHCNDSDKCLKVVADATVTIT SNKALKSQISALLSSIQNKAVADEKLTDQE 2>>>gi|10955264|ref|NP_052605.1| hypothetical protein pOSAK1_02 [Escherichia coli O157:H7 s 126 aa - 126 aa vs NC_009649.faa library

45119 residues in 180 sequences Expectation_n fit: rho(ln(x))= 7.1374+/-0.0246; mu= -7.6540+/- 1.313 mean_var=51.1189+/-13.171, 0’s: 0 Z-trim: 1 B-trim: 8 in 1/25 Lambda= 0.179384

FASTA (3.5 Sept 2006) function [optimized, BL50 matrix (15:-5)] ktup: 2 join: 36, opt: 24, open/ext: -10/-2, width: 16 Scan time: 0.000 The best scores are: opt bits E(180) gi|152973462|ref|YP_001338513.1| hypothetical prot ( 101) 58 22.9 0.29

>>>gi|10955264|ref|NP_052605.1|, 126 aa vs NC_009649.faa library ; pg_name: /opt/fasta/fasta34 ; pg_ver: 34.26 ; pg_argv: /opt/fasta/fasta34 -Q -H -E 1 -m 10 NC_002127.faa NC_009649.faa ; pg_name: FASTA ; pg_ver: 3.5 Sept 2006 ; pg_matrix: BL50 (15:-5) ; pg_open-ext: -10 -2 ; pg_ktup: 2 ; pg_optcut: 24 ; pg_cgap: 36 ; mp_extrap: 60000 180 ; mp_stats: Expectation_n fit: rho(ln(x))= 7.1374+/-0.0246; mu= -7.6540+/- 1.313 mean_var=51.1189+/-13.171, 0’s: 0 Z-trim: 1 B-trim: 8 in 1/25 Lambda= 0.179384 ; mp_KS: -0.0000 (N=0) at 8159228 >>gi|152973462|ref|YP_001338513.1| hypothetical protein KPN_pKPN3p05904 [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] ; fa_frame: f ; fa_initn: 50 ; fa_init1: 50 ; fa_opt: 58 ; fa_z-score: 95.8 ; fa_bits: 22.9 ; fa_expect: 0.29 ; sw_score: 58 ; sw_ident: 0.289 ; sw_sim: 0.632 ; sw_overlap: 38 >gi|10955264| .. ; sq_len: 126 ; sq_offset: 1 ; sq_type: p ; al_start: 1 ; al_stop: 38 ; al_display_start: 1 ———————————————MKKDKKYQIEAIKNKDKTLF IVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSF NGEKFSSYTLNKVTKTDEYN >gi|152973462|ref|YP_001338513.1| .. ; sq_len: 101 ; sq_type: p ; al_start: 44 ; al_stop: 81 ; al_display_start: 14 DALLGEIQRLRKQVHQLQLERDILTKANELIKKDLGVSFLKLKNREKTLI VDALKKKYPVAELLSVLQLARSCYFYQNVCTISMRKYA 3>>>gi|10955265|ref|NP_052606.1| hypothetical protein pOSAK1_03 [Escherichia coli O157:H7 s 346 aa - 346 aa vs NC_009649.faa library

45119 residues in 180 sequences Expectation_n fit: rho(ln(x))= 6.0276+/-0.0276; mu= 3.0670+/- 1.461 mean_var=37.1634+/- 8.980, 0’s: 0 Z-trim: 1 B-trim: 14 in 1/25 Lambda= 0.210386

FASTA (3.5 Sept 2006) function [optimized, BL50 matrix (15:-5)] ktup: 2 join: 37, opt: 25, open/ext: -10/-2, width: 16 Scan time: 0.020 The best scores are: opt bits E(180) gi|152973545|ref|YP_001338596.1| putative plasmid ( 242) 70 27.5 0.082

>>>gi|10955265|ref|NP_052606.1|, 346 aa vs NC_009649.faa library ; pg_name: /opt/fasta/fasta34 ; pg_ver: 34.26 ; pg_argv: /opt/fasta/fasta34 -Q -H -E 1 -m 10 NC_002127.faa NC_009649.faa ; pg_name: FASTA ; pg_ver: 3.5 Sept 2006 ; pg_matrix: BL50 (15:-5) ; pg_open-ext: -10 -2 ; pg_ktup: 2 ; pg_optcut: 25 ; pg_cgap: 37 ; mp_extrap: 60000 180 ; mp_stats: Expectation_n fit: rho(ln(x))= 6.0276+/-0.0276; mu= 3.0670+/- 1.461 mean_var=37.1634+/- 8.980, 0’s: 0 Z-trim: 1 B-trim: 14 in 1/25 Lambda= 0.210386 ; mp_KS: -0.0000 (N=0) at 8159228 >>gi|152973545|ref|YP_001338596.1| putative plasmid SOS inhibition protein A [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] ; fa_frame: f ; fa_initn: 52 ; fa_init1: 52 ; fa_opt: 70 ; fa_z-score: 105.5 ; fa_bits: 27.5 ; fa_expect: 0.082 ; sw_score: 70 ; sw_ident: 0.279 ; sw_sim: 0.651 ; sw_overlap: 43 >gi|10955265| .. ; sq_len: 346 ; sq_offset: 1 ; sq_type: p ; al_start: 197 ; al_stop: 238 ; al_display_start: 167 DFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKK QLSC-SLIMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNL GEYFTENKPKYIIREIHQET >gi|152973545|ref|YP_001338596.1| .. ; sq_len: 242 ; sq_type: p ; al_start: 52 ; al_stop: 94 ; al_display_start: 22 IMTVEEARQRGARLPSMPHVRTFLRLLTGCSRINSDVARRIPGIHRDPKD RLSSLKQVEEALDMLISSHGEYCPLPLTMDVQAENFPEVLHTRTVRRLKR QDFAFTRKMRREARQVEQSW >>><<<

579 residues in 3 query sequences 45119 residues in 180 library sequences Scomplib [34.26] start: Tue May 20 16:38:45 2008 done: Tue May 20 16:38:45 2008 Total Scan time: 0.020 Total Display time: 0.010

Function used was FASTA [version 34.26 January 12, 2007]