FASTA PARSABLE OUTPUT

Introduction

This document may be useful for programmers and script writers, but can be skipped by most users of the FastA program family (FastA, FastX, TFastA, TFastX, and SSearch).

The standard alignment formats of the FastA program family are difficult to parse, and so it has been hard to extract the alignment information from the output file for further processing. A new command-line parameter, -MARKx=10, saves the alignments in a format which is easily parsed. The following is a description of the parsable output file.

Records

The output file has three types of records. The header record starts with >>> . It contains information about the search as a whole, which version of the program was used, which analysis parameters were used, etc. There is only one header record per output file.

An alignment record contains information pertaining to a pairwise alignment, such as the scores for the alignment. It starts with >>. There will be one alignment record for each alignment that was saved.

Following each alignment record are two aligned sequence records, which start with > . Each of these records contains the information for one of the sequences in the alignment: the length of the sequence, the beginning and end of the alignment in that sequence's coordinates, etc.

The end of the parsable records is denoted with >>><<<.

Record Parameters

Information in each record consists of parameters and their values in a specific format. Parameters consist of a parameter tag, followed by an underscore, followed by the parameter's name. The complete format is:

; tag_name: value(s)

Parameters originating in William Pearson's FASTA package always have a two-character tag. Current FASTA tags are:

mp - main program information: name, version, statistical info, etc.
pg - program function information: function name and version, matrix used, etc.
fa - FastA results: scores, expect values, etc.
sw - Smith-Waterman results: scores, overlap values, etc.
sq - sequence information: length, type, etc.
al - alignment information: start, stop, display offset, etc.

Redistributors of the FASTA package may create their own parameters. If they do, they must use a tag with more than two characters, for example:

; ebi_access: M61687

; gcg_ver: 9.0

Currently there are no Accelrys GCG (GCG) specific parameters.

Interpreting Aligned Sequence Records

Most of the parameters specified by two-character tags correspond to values that are presented in other FastA output formats. A notable exception is parameters with the al tag:

al_start gives the location of the alignment start in the original sequence

al_stop gives the location of the end of the alignment in the original sequence

al_display_start gives the location of the first displayed residue in the original sequence. (This may not be the same as the first residue in the aligned region, because FastA provides some context for an alignment; even if the -SHOWall parameter is not used, FastA will try to provide about 30 residues on either side of the actual aligned region if the alignment is in the middle of one or the other sequence.)

Sequences may be padded with leading hyphens, if necessary. For example, if the beginning of the query sequence aligns with the tenth residue of the library sequence, then the query sequence will be padded with ten leading hyphens (-) to produce the alignment. The leading hyphens are a formatting convenience only; they are not considered in the numbering system foral_display_start, al_start, or al_stop.

As an example, here is a pair of aligned sequence records:

>gtm1_mouse ..

; sq_len: 217

; sq_offset: 1

; sq_type: p

; al_start: 3

; al_stop: 180

; al_display_start: 1

---PMILGYWNVRGLTHPIRMLLEYTDSSYDEKRYTMGDAPDFDRSQWLN

EKFKLGLDFPNLPYLIDGSHKITQSNAILRYLARKHH---LDGETEEERI

RADIVENQVMDTRMQLIMLCYNPDFEKQKPEFLKTIPEKMKLYSEFLGKR

PWFAGDKVTYVDFLAYDILDQYRMFEPKCLDA------FPNLRDFLARFE

GLKKISAYMKSSRYIATPIFSKMAHWSNK

>GTX2_TOBAC ..

; sq_len: 223

; sq_type: p

; al_start: 6

; al_stop: 181

; al_display_start: 1

MAEVKLLGFW-YSPFSHRVEWALKIKGVKYE---YIEEDRDN--KSSLLL

QSNPV---YKKVPVLIHNGKPIVESMIILEYIDETFEGPSILPKDPYDRA

LARFWAKFLDDKVAAVVNTFFRKGEEQEKGK--EEVYEMLKVLDNELKDK

KFFAGDKFGFADIAANLVGFWLGVFEEGYGDVLVKSEKFPNFSKWRDEYI

NCSQVNESLPPRDELLAFFRARFQAVVASRSAPK

To properly display this alignment, the first P of gtm1_mouse must line up with the first V in GTX2_TOBAC, and the actual aligned region (the region that scores as the best local alignment) starts with the first I in gtm1_mouse (amino acid 3) and the first L (amino acid 6) in GTX2_TOBAC.

An Example

Here is a printout of a complete parsable output file containing three alignment records, followed by a printout of the first alignment as it is output by FastA when the default parameter -MARKx=3 is used.

>>>A41264, 496 aa vs @GLUT4.LIST library

; mp_name: FASTA

; mp_ver: GCG Package 10.0 implementation of FASTA 3.1t12

; pg_name: FASTA

; pg_ver: 3.15 August, 1998

; pg_matrix: GenRunData:Blosum50.Cmp

; pg_gap-pen: -12 -2

; pg_ktup: 2

; pg_optcut: 25

; pg_cgap: 37

>>Pir2:A49158

; fa_initn: 1844

; fa_init1: 1201

; fa_opt: 1915

; sw_score: 1915

; sw_ident: 0.593

; sw_overlap: 496

>A41264 ..

; sq_len: 496

; sq_offset: 1

; sq_type: p

; al_start: 4

; al_stop: 493

; al_display_start: 1

-------------MADKKKITASLIYAVSVAAIGSLQFGYNTGVINAPEK

IIQAFYNRTLSQRSG----ETISPELLTSLWSLSVAIFSVGGMIGSFSVS

LFVNRFGRRNSMLLVNVLAFAGGALMALSKIAKAVEMLIIGRFIIGLFCG

LCTGFVPMYISEVSPTSLRGAFGTLNQLGIVVGILVAQIFGLEGIMGTEA

LWPLLLGFTIVPAVLQCVALLFCPESPRFLLINKMEEEKAQTVLQKLRGT

QDVSQDISEMKEESAKMSQEKKATVLELFRSPNYRQPIIISITLQLSQQL

SGINAVFYYSTGIFERAGITQPVYATIGAGVVNTVFTVVSLFLVERAGRR

TLHLVGLGGMAVCAAVMTIALALKEK--WIRYISIVATFGFVALFEIGPG

PIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGMLFPYAEKLCGPYVF

LIFLVFLLIFFIFTYFKVPETKGRTFEDISRGFEEQVETSSPSSPPIEKN

PMVEMNSIEPDKEVA

>A49158 ..

; sq_len: 509

; sq_type: p

; al_start: 17

; al_stop: 507

; al_display_start: 1

MPSGFQQIGSEDGEPPQQRVTGTLVLAVFSAVLGSLQFGYNIGVINAPQK

VIEQSYNETWLGRQGPEGPSSIPPGTLTTLWALSVAIFSVGGMISSFLIG

IISQWLGRKRAMLVNNVLAVLGGSLMGLANAAASYEMLILGRFLIGAYSG

LTSGLVPMYVGEIAPTHLRGALGTLNQLAIVIGILIAQVLGLESLLGTAS

LWPLLLGLTVLPALLQLVLLPFCPESPRYLYIIQNLEGPARKSLKRLTGW

ADVSGVLAELKDEKRKLERERPLSLLQLLGSRTHRQPLIIAVVLQLSQQL

SGINAVFYYSTSIFETAGVGQPAYATIGAGVVNTVFTLVSVLLVERAGRR

TLHLLGLAGMCGCAILMTVALLLLERVPAMSYVSIVAIFGFVAFFEIGPG

PIPWFIVAELFSQGPRPAAMAVAGFSNWTSNFIIGMGFQYVAEAMGPYVF

LLFAVLLLGFFIFTFLRVPETRGRTFDQISAAFHR-----TPSLLEQEVK

PSTELEYLGPDEND

>>Pir2:A32101

; fa_initn: 1822

; fa_init1: 1188

; fa_opt: 1883

; sw_score: 1883

; sw_ident: 0.589

; sw_overlap: 496

>A41264 ..

; sq_len: 496

; sq_offset: 1

; sq_type: p

; al_start: 4

; al_stop: 493

; al_display_start: 1

-------------MADKKKITASLIYAVSVAAIGSLQFGYNTGVINAPEK

IIQAFYNRTLSQRSG----ETISPELLTSLWSLSVAIFSVGGMIGSFSVS

LFVNRFGRRNSMLLVNVLAFAGGALMALSKIAKAVEMLIIGRFIIGLFCG

LCTGFVPMYISEVSPTSLRGAFGTLNQLGIVVGILVAQIFGLEGIMGTEA

LWPLLLGFTIVPAVLQCVALLFCPESPRFLLINKMEEEKAQTVLQKLRGT

QDVSQDISEMKEESAKMSQEKKATVLELFRSPNYRQPIIISITLQLSQQL

SGINAVFYYSTGIFERAGITQPVYATIGAGVVNTVFTVVSLFLVERAGRR

TLHLVGLGGMAVCAAVMTIALALKEKW--IRYISIVATFGFVALFEIGPG

PIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGMLFPYAEKLCGPYVF

LIFLVFLLIFFIFTYFKVPETKGRTFEDISRGFEEQVETSSPSSPPIEKN

PMVEMNSIEPDKEVA

>A32101 ..

; sq_len: 509

; sq_type: p

; al_start: 17

; al_stop: 507

; al_display_start: 1

MPSGFQQIGSEDGEPPQQRVTGTLVLAVFSAVLGSLQFGYNIGVINAPQK

VIEQSYNATWLGRQGPGGPDSIPQGTLTTLWALSVAIFSVGGMISSFLIG

IISQWLGRKRAMLANNVLAVLGGALMGLANAAASYEILILGRFLIGAYSG

LTSGLVPMYVGEIAPTHLRGALGTLNQLAIVIGILVAQVLGLESMLGTAT

LWPLLLAITVLPALLQLLLLPFCPESPRYLYIIRNLEGPARKSLKRLTGW

ADVSDALAELKDEKRKLERERPLSLLQLLGSRTHRQPLIIAVVLQLSQQL

SGINAVFYYSTSIFELAGVEQPAYATIGAGVVNTVFTLVSVLLVERAGRR

TLHLLGLAGMCGCAILMTVALLLLERVPSMSYVSIVAIFGFVAFFEIGPG

PIPWFIVAELFSQGPRPAAMAVAGFSNWTCNFIVGMGFQYVADAMGPYVF

LLFAVLLLGFFIFTFLRVPETRGRTFDQISATFRR-----TPSLLEQEVK

PSTELEYLGPDEND

>>Pir2:B30310

; fa_initn: 1796

; fa_init1: 1179

; fa_opt: 1862

; sw_score: 1862

; sw_ident: 0.585

; sw_overlap: 496

>A41264 ..

; sq_len: 496

; sq_offset: 1

; sq_type: p

; al_start: 4

; al_stop: 493

; al_display_start: 1

-------------MADKKKITASLIYAVSVAAIGSLQFGYNTGVINAPEK

IIQAFYNRTLSQRSG----ETISPELLTSLWSLSVAIFSVGGMIGSFSVS

LFVNRFGRRNSMLLVNVLAFAGGALMALSKIAKAVEMLIIGRFIIGLFCG

LCTGFVPMYISEVSPTSLRGAFGTLNQLGIVVGILVAQIFGLEGIMGTEA

LWPLLLGFTIVPAVLQCVALLFCPESPRFLLINKMEEEKAQTVLQKLRGT

QDVSQDISEMKEESAKMSQEKKATVLELFRSPNYRQPIIISITLQLSQQL

SGINAVFYYSTGIFERAGITQPVYATIGAGVVNTVFTVVSLFLVERAGRR

TLHLVGLGGMAVCAAVMTIALALKEKW--IRYISIVATFGFVALFEIGPG

PIPWFIVAELFSQGPRPAAMAVAGCSNWTSNFLVGMLFPYAEKLCGPYVF

LIFLVFLLIFFIFTYFKVPETKGRTFEDISRGFEEQVETSSPSSPPIEKN

PMVEMNSIEPDKEVA

>B30310 ..

; sq_len: 508

; sq_type: p

; al_start: 17

; al_stop: 506

; al_display_start: 1

MPSGFQQIGSDDGEPPRQRVTGTLVLAVFSAVLGSLQFGYNIGVINAPQK

VIEQSYNATWLGRQGPGGPDSIPQGTLTTLWALSVAIFSVGGMISSFLIG

IISQWLGRKRAMLANNVLAVLGGALMGLANAVASYEILILGRFLIGAYSG

LTSGLVPMYVGEIAPTHLRGALGTLNRLAIVIGILVAQVLGLESMLGTAT

LWPLLLALTVLPALLQLILLPFCPESPRYLYIIRNLEGPARKSLKPLTGW

ADVSDALAELKDEKRKLERERPMSLLQLLGSRTHRQPLIIAVVLQLSQQL

SGINAVFYYSTSIFESAGVGQPAYATIGAGVVNTVFTLVSVLLVERAGRR

TLHLLGLAGMCGCAILMTVALLLLERVPAMSYVSIVAIFGFVAFFEIGPG

PIPWF-VAELFSQGPRPAAMAVAGFSNWTCNFIVGMGFQYVADRMGPYVF

LLFAVLLLGFFIFTFLKVPETRGRTFDQISAAFRR-----TPSLLEQEVK

PSTELEYLGPDEND

>>><<<

------------------------------------------------------------------------------

SCORES Init1: 1201 Initn: 1844 Opt: 1915

Smith-Waterman score: 1915; 59.3% identity in 496 aa overlap

10 20 30 40

A41264 MADKKKITASLIYAVSVAAIGSLQFGYNTGVINAPEKIIQAFYNRTL

::::|::|: || |::|||||||| ||||||:|:|: ||:|

A49158 MPSGFQQIGSEDGEPPQQRVTGTLVLAVFSAVLGSLQFGYNIGVINAPQKVIEQSYNETW

10 20 30 40 50 60

50 60 70 80 90 100

A41264 SQRSG----ETISPELLTSLWSLSVAIFSVGGMIGSFSVSLFVNRFGRRNSMLLVNVLAF

|:| :| | ||:||:||||||||||||:|| :::: : :||: :||: ||||

A49158 LGRQGPEGPSSIPPGTLTTLWALSVAIFSVGGMISSFLIGIISQWLGRKRAMLVNNVLAV

70 80 90 100 110 120

110 120 130 140 150 160

A41264 AGGALMALSKIAKAVEMLIIGRFIIGLFCGLCTGFVPMYISEVSPTSLRGAFGTLNQLGI

||:||:|:: | : ||||:|||:|| : || :|:||||::|::|| ||||:||||||:|

A49158 LGGSLMGLANAAASYEMLILGRFLIGAYSGLTSGLVPMYVGEIAPTHLRGALGTLNQLAI

130 140 150 160 170 180

170 180 190 200 210 220

A41264 VVGILVAQIFGLEGIMGTEALWPLLLGFTIVPAVLQCVALLFCPESPRFLLINKMEEEKA

|:|||:||::|||:::|| :|||||||:|::||:|| | | |||||||:| | : | |

A49158 VIGILIAQVLGLESLLGTASLWPLLLGLTVLPALLQLVLLPFCPESPRYLYIIQNLEGPA

190 200 210 220 230 240

230 240 250 260 270 280

A41264 QTVLQKLRGTQDVSQDISEMKEESAKMSQEKKATVLELFRSPNYRQPIIISITLQLSQQL

: |::| | ||| ::|:|:|: |: :|: ::|:|: | ::|||:||:::|||||||

A49158 RKSLKRLTGWADVSGVLAELKDEKRKLERERPLSLLQLLGSRTHRQPLIIAVVLQLSQQL

250 260 270 280 290 300

290 300 310 320 330 340

A41264 SGINAVFYYSTGIFERAGITQPVYATIGAGVVNTVFTVVSLFLVERAGRRTLHLVGLGGM

|||||||||||:||| ||: ||:||||||||||||||:||::||||||||||||:||:||

A49158 SGINAVFYYSTSIFETAGVGQPAYATIGAGVVNTVFTLVSVLLVERAGRRTLHLLGLAGM

310 320 330 340 350 360

350 360 370 380 390 400

A41264 AVCAAVMTIALALKEK--WIRYISIVATFGFVALFEIGPGPIPWFIVAELFSQGPRPAAM

|| :||:|| | |: : |:|||| |||||:||||||||||||||||||||||||||

A49158 CGCAILMTVALLLLERVPAMSYVSIVAIFGFVAFFEIGPGPIPWFIVAELFSQGPRPAAM

370 380 390 400 410 420

410 420 430 440 450 460

A41264 AVAGCSNWTSNFLVGMLFPYAEKLCGPYVFLIFLVFLLIFFIFTYFKVPETKGRTFEDIS

|||| |||||||::|| | |: : ||||||:| |:|| |||||:::||||:||||::||

A49158 AVAGFSNWTSNFIIGMGFQYVAEAMGPYVFLLFAVLLLGFFIFTFLRVPETRGRTFDQIS

430 440 450 460 470 480

470 480 490

A41264 RGFEEQVETSSPSSPPIEKNPMVEMNSIEPDKEVA

:|:: :|| | :| :|:: : ||::

A49158 AAFHR-----TPSLLEQEVKPSTELEYLGPDEND

490 500

Printed: May 27, 2005 12:12

Technical Support: support-us@accelrys.com, support-japan@accelrys.com,
or support-eu@accelrys.com

Licenses and Trademarks: Discovery Studio ®, SeqLab ®, SeqWeb ®, SeqMerge ®, GCG ® and, the GCG logo are registered trademarks of Accelrys Inc.

All other product names mentioned in this documentation may be trademarks, and if so, are trademarks or registered trademarks of their respective holders and are used in this documentation for identification purposes only.