This is just the standard FASTA sequence format (Section A.1, “Supported Sequence Formats”) with gaps, where many sequences are concatenated. FASTA format is used by Bill Pearson's suite of FASTA programs. For further information see:
| http://rcr-www.med.nyu.edu/rcr/fastaman.html |
>IXI_234 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG PPAWAGDRSHE >IXI_235 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTC TTSTSTRHRGRSGW----------RASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTG PPAWAGDRSHE >IXI_236 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQATGGWKTCSGTC TTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--GSRPPRFAPPLMSSCITSTTG PPPPAGDRSHE >IXI_237 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQATGGYKTCSGTC TTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--GSRPNRFAPTLMSSCLTSTTG PPAYAGDRSHE
This is the standard default output format used by Bill Pearson's suite of FASTA programs. For further information see:
| http://rcr-www.med.nyu.edu/rcr/fastaman.html |
########################################
# Program: water
# Rundate: Wed Jan 16 17:21:36 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: IXI_234
# 2: IXI_235
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity: 112/131 (85.5%)
# Similarity: 112/131 (85.5%)
# Gaps: 19/131 (14.5%)
# Score: 591.5
#
#
#=======================================
10 20 30 40 50
IXI_23 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT
::::::::::::::: ::::::::::::::::::::::::::
IXI_23 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT
10 20 30 40
60 70 80 90 100
IXI_23 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG
:::::::::::::::::::::::: ::::::::::::::::
IXI_23 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG
50 60 70 80
110 120 130
IXI_23 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE
:::::::::::::::::::::::::::::::
IXI_23 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE
90 100 110
#---------------------------------------
#--------------------------------------- This is an alternative output format used by Bill Pearson's suite of FASTA programs in which identities are not marked. Instead, conservative replacements are denoted by 'x' and non-conservative substitutions by 'X'. For further information see:
| http://rcr-www.med.nyu.edu/rcr/fastaman.html |
########################################
# Program: water
# Rundate: Wed Jan 16 17:22:07 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: IXI_234
# 2: IXI_235
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity: 112/131 (85.5%)
# Similarity: 112/131 (85.5%)
# Gaps: 19/131 (14.5%)
# Score: 591.5
#
#
#=======================================
10 20 30 40 50
IXI_23 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT
IXI_23 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT
10 20 30 40
60 70 80 90 100
IXI_23 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG
IXI_23 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG
50 60 70 80
110 120 130
IXI_23 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE
IXI_23 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE
90 100 110
#---------------------------------------
#--------------------------------------- This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the residues in the second sequence are only shown if they are different from the first. For further information see:
| http://rcr-www.med.nyu.edu/rcr/fastaman.html |
########################################
# Program: water
# Rundate: Wed Jan 16 17:22:25 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: IXI_234
# 2: IXI_235
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity: 112/131 (85.5%)
# Similarity: 112/131 (85.5%)
# Gaps: 19/131 (14.5%)
# Score: 591.5
#
#
#=======================================
10 20 30 40 50
IXI_23 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT
IXI_23 ...............---------..........................
60 70 80 90 100
IXI_23 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG
IXI_23 ........................----------................
110 120 130
IXI_23 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE
IXI_23 ...............................
#---------------------------------------
#--------------------------------------- This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the aligned sequences are displayed in FASTA sequence format. These can be used to build a primitive multiple alignment. For further information see:
| http://rcr-www.med.nyu.edu/rcr/fastaman.html |
######################################## # Program: water # Rundate: Wed Jan 16 17:22:42 2002 # Report_file: stdout ######################################## #======================================= # # Aligned_sequences: 2 # 1: IXI_234 # 2: IXI_235 # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 131 # Identity: 112/131 (85.5%) # Similarity: 112/131 (85.5%) # Gaps: 19/131 (14.5%) # Score: 591.5 # # #======================================= >IXI_234 .. TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE >IXI_235 .. TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE #--------------------------------------- #---------------------------------------
This is an alternative output format used by Bill Pearson's suite of FASTA programs in which the aligned sequences are displayed in FASTA sequence format and the sequence length, alignment start and stop information are given in lines starting with a ';' character just after the title line for each sequence. It is intended to be easily parsed by other programs. For further information see:
| http://rcr-www.med.nyu.edu/rcr/fastaman.html |
######################################## # Program: water # Rundate: Wed Jan 16 17:23:00 2002 # Report_file: stdout ######################################## #======================================= # # Aligned_sequences: 2 # 1: IXI_234 # 2: IXI_235 # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 131 # Identity: 112/131 (85.5%) # Similarity: 112/131 (85.5%) # Gaps: 19/131 (14.5%) # Score: 591.5 # # #======================================= >IXI_234 .. ; sq_len: 131 ; al_start: 1 ; al_stop: 131 ; al_display_start: 1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT-GGWKTCSGTCTTSTSTRHRGRSGWSARTT TAACLRASRKSMRAACSRSAG-SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE- >IXI_235 .. ; sq_len: 131 ; al_start: 1 ; al_stop: 131 ; al_display_start: 1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE #--------------------------------------- #---------------------------------------
This is a format defined by EMBOSS in which the start and end of matches between pairs of sequences are highlighted.
131 IXI_234 + 1..131 IXI_235 + 1..131 #--------------------------------------- #---------------------------------------
MSF is the format used for multiple sequences by the Accelrys GCG, formerly known as the GCG Wisconsin, package. GCG was a commercial software package of programs and utilities for gene and protein analysis. For further information see:
| http://www.accelrys.com/products/gcg/ |
!!AA_MULTIPLE_ALIGNMENT 1.0
stdout MSF: 131 Type: P 16/01/02 CompCheck: 3003 ..
Name: IXI_234 Len: 131 Check: 6808 Weight: 1.00
Name: IXI_235 Len: 131 Check: 4032 Weight: 1.00
Name: IXI_236 Len: 131 Check: 2744 Weight: 1.00
Name: IXI_237 Len: 131 Check: 9419 Weight: 1.00
//
1 50
IXI_234 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT
IXI_235 TSPASIRPPAGPSSR.........RPSPPGPRRPTGRPCCSAAPRRPQAT
IXI_236 TSPASIRPPAGPSSRPAMVSSR..RPSPPPPRRPPGRPCCSAAPPRPQAT
IXI_237 TSPASLRPPAGPSSRPAMVSSRR.RPSPPGPRRPT....CSAAPRRPQAT
51 100
IXI_234 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG
IXI_235 GGWKTCSGTCTTSTSTRHRGRSGW..........RASRKSMRAACSRSAG
IXI_236 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR..G
IXI_237 GGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR..G
101 131
IXI_234 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE
IXI_235 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE
IXI_236 SRPPRFAPPLMSSCITSTTGPPPPAGDRSHE
IXI_237 SRPNRFAPTLMSSCLTSTTGPPAYAGDRSHESimple format for multiple sequences. This format displays the sequence names, positions and sequences and then puts the markup line underneath the sequences.
########################################
# Program: demoalign
# Rundate: Thu 18 Mar 2010 10:03:39
# Commandline: demoalign
# [-sequence] Msf
# [-outfile] Multiple
# -aformat2 multiple
# Align_format: multiple
# Report_file: Multiple
########################################
#=======================================
#
# Aligned_sequences: 4
# 1: IXI_234
# 2: IXI_235
# 3: IXI_236
# 4: IXI_237
# Matrix: EBLOSUM62
# Gap_penalty: 9
# Extend_penalty: -1
#
# Length: 131
# Identity: 95/131 (72.5%)
# Similarity: 127/131 (96.9%)
# Gaps: 25/131 (19.1%)
#
#
#=======================================
IXI_234 1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT 50
IXI_235 1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT 41
IXI_236 1 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQAT 48
IXI_237 1 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQAT 45
|||||:|||||||||::::::: |||||:||||:::::|||||:|||||
IXI_234 51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG 100
IXI_235 42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG 81
IXI_236 49 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--G 96
IXI_237 46 GGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--G 93
||:||||||||||||||||||||:::::::::::||||||||||||| |
IXI_234 101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 131
IXI_235 82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 112
IXI_236 97 SRPPRFAPPLMSSCITSTTGPPPPAGDRSHE 127
IXI_237 94 SRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE 124
|||:||||:|||||:|||||||::|||||||
#---------------------------------------
#---------------------------------------
This is the default format used when there are only 2 sequences. When "simple" format is selected but there are only 2 sequences, then this format is used. The sequences have a markup line between them.
########################################
# Program: water
# Rundate: Wed Jan 16 17:23:19 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: IXI_234
# 2: IXI_235
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity: 112/131 (85.5%)
# Similarity: 112/131 (85.5%)
# Gaps: 19/131 (14.5%)
# Score: 591.5
#
#
#=======================================
IXI_234 1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT 50
||||||||||||||| ||||||||||||||||||||||||||
IXI_235 1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT 41
IXI_234 51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG 100
|||||||||||||||||||||||| ||||||||||||||||
IXI_235 42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG 81
IXI_234 101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 131
|||||||||||||||||||||||||||||||
IXI_235 82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 112
#---------------------------------------
#--------------------------------------- This does not display the sequence alignment. It shows only the names of the sequences, the length of the alignment and the score.
IXI_234 IXI_235 131 (100.0) #--------------------------------------- #---------------------------------------
Simple format is known by the synonyms simple, multiple and unknown. This format displays the sequence names, positions and sequences and then puts the markup line underneath the sequences. When multiple sequences are aligned then the format is identical to "Multiple' format. When only two sequences are aligned then the format is identical to the "Pair" format.
This is the format used by the SRS system. SRS is a scalable and robust platform that provides fast access to diverse data resources in the life sciences from public and proprietary sources. For further information see:
| http://www.biowisdom.com/solutions/srs/ |
The SRS format shows the sequence ID name, the sequence position and the sequence.
######################################## # Program: alignret # Rundate: Wed Jan 16 17:18:29 2002 # Report_file: stdout ######################################## #======================================= # # Aligned_sequences: 4 # 1: IXI_234 # 2: IXI_235 # 3: IXI_236 # 4: IXI_237 # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 131 # Identity: 95/131 (72.5%) # Similarity: 127/131 (96.9%) # Gaps: 25/131 (19.1%) # Score: 100.0 # # #======================================= IXI_234 1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT 50 IXI_235 1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT 41 IXI_236 1 TSPASIRPPAGPSSRPAMVSSR--RPSPPPPRRPPGRPCCSAAPPRPQAT 48 IXI_237 1 TSPASLRPPAGPSSRPAMVSSRR-RPSPPGPRRPT----CSAAPRRPQAT 45 IXI_234 51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG 100 IXI_235 42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG 81 IXI_236 49 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSR--G 96 IXI_237 46 GGYKTCSGTCTTSTSTRHRGRSGYSARTTTAACLRASRKSMRAACSR--G 93 IXI_234 101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 131 IXI_235 82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 112 IXI_236 97 SRPPRFAPPLMSSCITSTTGPPPPAGDRSHE 127 IXI_237 94 SRPNRFAPTLMSSCLTSTTGPPAYAGDRSHE 124 #--------------------------------------- #---------------------------------------
This is the format used by the SRS system for pairwise alignments. It is similar in style to "pair" format.
########################################
# Program: water
# Rundate: Wed Jan 16 17:23:40 2002
# Report_file: stdout
########################################
#=======================================
#
# Aligned_sequences: 2
# 1: IXI_234
# 2: IXI_235
# Matrix: EBLOSUM62
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 131
# Identity: 112/131 (85.5%)
# Similarity: 112/131 (85.5%)
# Gaps: 19/131 (14.5%)
# Score: 591.5
#
#
#=======================================
IXI_234 1 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQAT 50
||||||||||||||| ||||||||||||||||||||||||||
IXI_235 1 TSPASIRPPAGPSSR---------RPSPPGPRRPTGRPCCSAAPRRPQAT 41
IXI_234 51 GGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAG 100
|||||||||||||||||||||||| ||||||||||||||||
IXI_235 42 GGWKTCSGTCTTSTSTRHRGRSGW----------RASRKSMRAACSRSAG 81
IXI_234 101 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 131
|||||||||||||||||||||||||||||||
IXI_235 82 SRPNRFAPTLMSSCITSTTGPPAWAGDRSHE 112
#---------------------------------------
#--------------------------------------- The alignment used by the TCOFFEE package. TCOFFEE is a collection of tools for computing, evaluating and manipulating multiple alignments of DNA, protein sequences and structures. For further information see:
| http://www.igs.cnrs-mrs.fr/Tcoffee/tcoffee_cgi/index.cgi |
2 IXI_234 131 TSPASIRPPAGPSSRPAMVSSRRTRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWSARTTTAACLRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE IXI_235 112 TSPASIRPPAGPSSRRPSPPGPRRPTGRPCCSAAPRRPQATGGWKTCSGTCTTSTSTRHRGRSGWRASRKSMRAACSRSAGSRPNRFAPTLMSSCITSTTGPPAWAGDRSHE ! score=591.5 ! matrix=EBLOSUM62 ! gapopen=10.0 gapext=0.5 #1 2 1 1 0 1 0 2 2 0 1 0 3 3 0 1 0 4 4 0 1 0 5 5 0 1 0 6 6 0 1 0 ... < data omitted for brevity > 125 106 0 1 0 126 107 0 1 0 127 108 0 1 0 128 109 0 1 0 129 110 0 1 0 130 111 0 1 0 131 112 0 1 0 ! SEQ_1_TO_N
This is a special verbose format for use in debugging. It might be useful to software developers but not for typical users of EMBOSS.
Trace output ============ a: Type:'P' Formatstr:'debug' Format:15 b: File:Trace Show: ShowAcc:No ShowDes:No ShowUsa:No Booleans: Multi:No Global:No SeqOnly:No SeqExternal:No Numbers: NMin:0 NMax:0 Nseqs:4 Count:0 Width:50 Matrices: IMatrix:'EBLOSUM62'(25) FMatrix:''(0) Strings: Matrix:'EBLOSUM62' GapPen:'9' ExtPen:'-1' Header: '<null>' SubHeader: '<null>' Tail: '<null>' SubTail: '<null>' Key: seqlen/len offset> start..end <offend (suboffset) rev Begin..End GapBegin..End align0: Nseqs:4 LenAli:131 NumId:0 NumSim:0 NumGap:0 Score:'<null>' fixed0: Nseqs:4 LenAli:131 NumId:95 NumSim:127 NumGap:25 Score:'<null>' Num0.0: 131/131 0> 1..131 <0 (0) Rev:No 1..131 0..0 Seq0.0: 131 'TSPASIRPPAGPSSRPAMVS...SSCITSTTGPPAWAGDRSHE' Num0.1: 112/112 0> 1..131 <0 (0) Rev:No 1..131 0..0 Seq0.1: 131 'TSPASIRPPAGPSSR-----...SSCITSTTGPPAWAGDRSHE' Num0.2: 127/127 0> 1..131 <0 (0) Rev:No 1..131 0..0 Seq0.2: 131 'TSPASIRPPAGPSSRPAMVS...SSCITSTTGPPPPAGDRSHE' Num0.3: 124/124 0> 1..131 <0 (0) Rev:No 1..131 0..0 Seq0.3: 131 'TSPASLRPPAGPSSRPAMVS...SSCLTSTTGPPAYAGDRSHE' #--------------------------------------- #---------------------------------------