Table of Contents
A2M
Each sequence is represented by two lines:
- The first line starts with > followed by the sequence identifier and some other remarks.
- The second line contains the aligned residues; Alignments are shown with:
- Inserts as lower case characters,
- Matches as upper case characters,
- Deletions as ' - ', and
- Gaps aligned to inserts as ' . '
Example
>T1152
MY...TVKPGDT......MWKIAV...K..YQI...GI.....SEIIAANPQIKNPNLIYPGQKINIPNILEHHHHHH
>MTBAKSStandDraft_2_1061841.scaffolds.fasta_scaffold367497_1
TY...D-KDGYR......HYRTRV...Y..YTL...RR.....NEDNALIA-REVFSQVYKKEAL-CPIA--------
>ETNvirnome_2_130_1030620.scaffolds.fasta_scaffold104244_1
G-...EREKGR-......--HSKS...R..QEK...GF.....KEKK---P-TKKPSATNKPVNTAKPAA--------
>tr|A0A235B7N0|A0A235B7N0_9BACL Uncharacterized protein OS=Paludifilum halophilum OX=1642702
EAsavDRITSDSilenfvQWIFSE...E..KEVeekHT.....EESVQPTPAVKHSPDSSGSSKSSSSD---------
>tr|A0A1E5LFN5|A0A1E5LFN5_9BACI Uncharacterized protein OS=Bacillus solimangrovi OX=1305675
SA...KVKRGRT......FIPLRSateSfgYDV...IWkenenAVYLKSNPTIKPKDSTQ------------------
A3M
It is almost like A2M format. The only difference is that Gaps aligned to inserts ('.') can be excluded, and one could view the A3M format as a more method method for representing an MSA compared to FASTA or A2M.
Example
>T1152
MYTVKPGDTMWKIAVKYQIGISEIIAANPQIKNPNLIYPGQKINIPNILEHHHHHH
>MTBAKSStandDraft_2_1061841.scaffolds.fasta_scaffold367497_1
TYD-KDGYRHYRTRVYYTLRRNEDNALIA-REVFSQVYKKEAL-CPIA--------
>ETNvirnome_2_130_1030620.scaffolds.fasta_scaffold104244_1
G-EREKGR---HSKSRQEKGFKEKK---P-TKKPSATNKPVNTAKPAA--------
>tr|A0A235B7N0|A0A235B7N0_9BACL Uncharacterized protein OS=Paludifilum halophilum OX=1642702
EAsavDRITSDSilenfvQWIFSEEKEVeekHTEESVQPTPAVKHSPDSSGSSKSSSSD---------
>tr|A0A1E5LFN5|A0A1E5LFN5_9BACI Uncharacterized protein OS=Bacillus solimangrovi OX=1305675
SAKVKRGRTFIPLRSateSfgYDVIWkenenAVYLKSNPTIKPKDSTQ------------------
Fasta
Sequences are separated by '>'. The remaining lines before next '>' contain the aligned sequence, which:
- lower and upper case are equivalent;
- ' . ' and ' - ' are equivalent. Aligned => Sequences have the same length.
Example
>T1152
MY---TVKPGDT------MWKIAV---K--YQI---GI-----SEIIAANPQIKNPNLIYPGQKINIPNILEHHHHHH
>MTBAKSStandDraft_2_1061841.scaffolds.fasta_scaffold367497_1
TY---D-KDGYR------HYRTRV---Y--YTL---RR-----NEDNALIA-REVFSQVYKKEAL-CPIA--------
>ETNvirnome_2_130_1030620.scaffolds.fasta_scaffold104244_1
G----EREKGR---------HSKS---R--QEK---GF-----KEKK---P-TKKPSATNKPVNTAKPAA--------
>tr|A0A235B7N0|A0A235B7N0_9BACL Uncharacterized protein OS=Paludifilum halophilum OX=1642702
EASAVDRITSDSILENFVQWIFSE---E--KEVEEKHT-----EESVQPTPAVKHSPDSSGSSKSSSSD---------
>tr|A0A1E5LFN5|A0A1E5LFN5_9BACI Uncharacterized protein OS=Bacillus solimangrovi OX=1305675
SA---KVKRGRT------FIPLRSATESFGYDV---IWKENENAVYLKSNPTIKPKDSTQ------------------
STO (Stockholm)
It consists of:
- A header line containing format and version information.
- Mark-up lines that start with "#=GF," "#=GC," "#=GS," or "#=GR."
- Alignment lines featuring the sequence name and its corresponding aligned sequence. Within these lines:
- Inserts are represented as lowercase characters,
- Matches are indicated by uppercase characters, and
- Gaps are denoted by either ' . ' or ' - '.
Additionally, the "//" line indicates the end of the alignment. Sequences in this format are divided into segments of 200 characters.
Example
# STOCKHOLM 1.0
#=GF ID T1152
#=GS T1152
#=GS MTBAKSStandDraft_2_1061841.scaffolds.fasta_scaffold367497_1
#=GS ETNvirnome_2_130_1030620.scaffolds.fasta_scaffold104244_1
#=GS tr|A0A235B7N0|A0A235B7N0_9BACL Uncharacterized protein OS=Paludifilum halophilum OX=1642702
#=GS tr|A0A1E5LFN5|A0A1E5LFN5_9BACI Uncharacterized protein OS=Bacillus solimangrovi OX=1305675
T1152 MY---TVKPGDT------MWKIAV---K--YQI---GI-----SEIIAANPQIKNPNLIYPGQKINIPNILEHHHHHH
MTBAKSStandDraft_2_1061841.scaffolds.fasta_scaffold367497_1 TY---D-KDGYR------HYRTRV---Y--YTL---RR-----NEDNALIA-REVFSQVYKKEAL-CPIA--------
ETNvirnome_2_130_1030620.scaffolds.fasta_scaffold104244_1 G----EREKGR---------HSKS---R--QEK---GF-----KEKK---P-TKKPSATNKPVNTAKPAA--------
tr|A0A235B7N0|A0A235B7N0_9BACL EASAVDRITSDSILENFVQWIFSE---E--KEVEEKHT-----EESVQPTPAVKHSPDSSGSSKSSSSD---------
tr|A0A1E5LFN5|A0A1E5LFN5_9BACI SA---KVKRGRT------FIPLRSATESFGYDV---IWKENENAVYLKSNPTIKPKDSTQ------------------
//
ALN
It only consists of aligned sequences, each on a separate line, and the initial sequence is gap-free.
Example
MYTVKPGDTMWKIAVKYQIGISEIIAANPQIKNPNLIYPGQKINIPNILEHHHHHH
TYD-KDGYRHYRTRVYYTLRRNEDNALIA-REVFSQVYKKEAL-CPIA--------
G-EREKGR---HSKSRQEKGFKEKK---P-TKKPSATNKPVNTAKPAA--------
EADRITSDSQWIFSEEKEVHTEESVQPTPAVKHSPDSSGSSKSSSSD---------
SAKVKRGRTFIPLRSSYDVIWAVYLKSNPTIKPKDSTQ------------------
CLUSTAL
Clustal is commonly associated with the Clustal series of programs for sequence alignment. The Clustal MSA format typically begins with a header line that provides information about the alignment.
Following the header, Clustal format represents each sequence as a pair of columns in a line.
- The first column contains the sequence name or identifier,
- The second column contains the aligned sequence, which:
- Gaps are shown as '-'
- Matches are shown as uppercase letters.
Sequences in this format are divided into segments of 60 characters.
Example
Generated CLUSTAL format
T1152 MY---TVKPGDT------MWKIAV---K--YQI---GI-----SEIIAANPQIKNPNLIY
MTBAKSStandDraft_2_1061841.scaffolds.fasta_scaffold367497_1 TY---D-KDGYR------HYRTRV---Y--YTL---RR-----NEDNALIA-REVFSQVY
ETNvirnome_2_130_1030620.scaffolds.fasta_scaffold104244_1 G----EREKGR---------HSKS---R--QEK---GF-----KEKK---P-TKKPSATN
tr|A0A235B7N0|A0A235B7N0_9BACL EASAVDRITSDSILENFVQWIFSE---E--KEVEEKHT-----EESVQPTPAVKHSPDSS
tr|A0A1E5LFN5|A0A1E5LFN5_9BACI SA---KVKRGRT------FIPLRSATESFGYDV---IWKENENAVYLKSNPTIKPKDSTQ
T1152 PGQKINIPNILEHHHHHH
MTBAKSStandDraft_2_1061841.scaffolds.fasta_scaffold367497_1 KKEAL-CPIA--------
ETNvirnome_2_130_1030620.scaffolds.fasta_scaffold104244_1 KPVNTAKPAA--------
tr|A0A235B7N0|A0A235B7N0_9BACL GSSKSSSSD---------
tr|A0A1E5LFN5|A0A1E5LFN5_9BACI ------------------
PFAM
It's similar to Clustal in the sense that it separates sequence identifiers and sequences with a tab, but unlike Clustal, the sequences are not uniformly indented. Additionally, it doesn't split sequences into 60-character segments, as Clustal does. Also, it does not contain header line.
Example
T1152 MY---TVKPGDT------MWKIAV---K--YQI---GI-----SEIIAANPQIKNPNLIYPGQKINIPNILEHHHHHH
MTBAKSStandDraft_2_1061841.scaffolds.fasta_scaffold367497_1 TY---D-KDGYR------HYRTRV---Y--YTL---RR-----NEDNALIA-REVFSQVYKKEAL-CPIA--------
ETNvirnome_2_130_1030620.scaffolds.fasta_scaffold104244_1 G----EREKGR---------HSKS---R--QEK---GF-----KEKK---P-TKKPSATNKPVNTAKPAA--------
tr|A0A235B7N0|A0A235B7N0_9BACL EASAVDRITSDSILENFVQWIFSE---E--KEVEEKHT-----EESVQPTPAVKHSPDSSGSSKSSSSD---------
tr|A0A1E5LFN5|A0A1E5LFN5_9BACI SA---KVKRGRT------FIPLRSATESFGYDV---IWKENENAVYLKSNPTIKPKDSTQ------------------
For further assistance or inquiries, please contact the developer or create an issue in the GitHub repository.
1.11.0