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RID
26FSE6M6114 (Expires on 11-10 22:21 pm)
Query ID
EU998907.1
Description
Buchnera aphidicola (Brachycaudus rumexicolens) single-strand binding protein (ssb)
gene, partial cds; ssb-dnaB intergenic spacer, complete sequence; and DnaB (dnaB) gene,
partial cds
Molecule type
nucleic acid
Query
Length
528
EU998905.1
Buchnera aphidic
(Brachycaudus
helichrysi) single
strand binding
spacer, complete
sequence; and D
(dnaB) gene, pa
cds
nucleic acid
597
BLASTN
2.5.1+ Citation
Other reports: Search Summary
Graphic Summary
Distribution of 1 Blast Hits on the Query Sequence
Mouse over to see the title, click to show alignments
1
100
200
300
400
500
Description
Buchnera aphidicola (Brachycaudus helichrysi) single-strand binding protein (ssb) gene, partial cds; ssb-d
(dnaB) gene, partial cds
Alignments
DownloadGenBankGraphicsNextPreviousDescriptions
Related Information
Range 1: 39 to 556GenBankGraphicsNext MatchPrevious Match
Alignment statistics for match #1
Score
Expect
Identities
Gaps
Strand
333 bits(180)
1e-95
430/544(79%)
43/544(7%)
Plus/Plu
Query
CCTCTACTAGCCATATCAAAACTCCACTTCTaaaatatgaaaaaacaaacaatatatttt
|||||||||||||||
|||||||||||||||||| ||
|| ||| |||| |
60
Sbjct
39
CCTCTACTAGCCATAGTAAAACTCCACTTCTAAAACAT--ATGAAGAAA-AATA-A---T
91
Query
61
ataaatttttattatacatcgtaaatattttatttaGTATGATCCAAACTATAAAAAATG
120
||
| |||||||||||||||||||||||||||||||||||||| |||||||||||||||
Sbjct
92
AT--A-TTTTATTATACATCGTAAATATTTTATTTAGTATGATCTAAACTATAAAAAATG
148
Query
121
CTATATTATTTTTAATGTGttaaaaaca-ct-attacttaaattatgaaaaactcttatt
178
||||||||||
||||| | || || |||||||
|| ||| |||||||||
Sbjct
149
GTATATTATTT-------G--AAAAATATCTCATAACTTAAACCATTAAACACTCTTATT
199
Query
179
-aaaatgtattcttacta-aaaaatata-attatttttctaaaaaattaaaaattagata
235
|| || ||| |||||||
| |||||| |
| | |
| | |||||||
||| |
Sbjct
200
CAACATTTATACTTACTATCATAATATACAAAAATATAAT-TATATTTAAAAA-AAGA-A
256
Query
236
agaaaatatcaataataaatagttatatcttat-aaa-a-aat-cttatagaatacgaga
291
||
||| | || || |
Sbjct
257
AAAAGAAATAAACAATAAATAATCATGTCTTATTAAATACGATAAAAATAAATTAAGATA
316
Query
292
a---aaataaaatcttat-a--agctatatataaataattttttatgcttatattaatga
345
| ||||||| | || |
|| ||||
|||||||||||
|||| |||
||
Sbjct
317
ATCTATATAAAATTTAATCATTAAATACATAT-GATAATTTTTTACTTTTATGTTACAGA
375
Query
346
t--aaaaaattaaaataaattaaaaaaaGGACTTAAATAGATTAGTCCCCAGATAGTGTA
403
|||||| |||||
||||||||||
Sbjct
376
TAGAAAAAACTAAAAACAATT-AGAAAAGGACTTAAATAGATTAATCCGTAGATAGTGTA
434
Query
404
TTATTGCAATATTACGATATATAATTTTGTAGaaattaactaaataatggtatatgcaat
463
||||||||||||||||
|||||||||| |||||||||||||||||||||||||||||||
Sbjct
435
TTATTGCAATATTACG--ATATAATTTTATAGAAATTAACTAAATAATGGTATATGCAAT
492
Query
464
aaatatggctaaaaataaattatatttaaatcaaattaacagattaaaaattCCACCACA
523
493
||||| |||||||||||
AAATATGGCTAAAAACAAATTATATTTAAATGAAATTAACAAGTTAAAGATTCCACCACA
552
Query
524
TTCT
527
||||
Sbjct
553
TTCT
556
FASTA format
From Wikipedia, the free encyclopedia
1History
2Description line
o
2.1Sequence representation
3Sequence identifiers
3.1Compression
3.2File extension
4See also
5References
6External links
History[edit]
The original FASTA/Pearson format is described in the documentation for the FASTA suite of
programs. It can be downloaded with any free distribution of FASTA (see fasta20.doc,
fastaVN.doc or fastaVN.mewhere VN is the Version Number).
A sequence in FASTA format is represented as a series of lines, each of which should be no
longer than 120 characters and usually do not exceed 80 characters. This probably was to allow
for preallocation of fixed line sizes in software: at the time most users relied on DEC VT (or
compatible) terminals which could display 80 or 132 characters per line. Most people preferred
the bigger font in 80-character modes and so it became the recommended fashion to use 80
characters or less (often 70) in FASTA lines. Also, the width of a standard printed page is 70 to
80 characters (depending on the font).
The first line in a FASTA file starts either with a ">" (greater-than) symbol or, less frequently, a ";"
(semicolon) and was taken as a comment. Subsequent lines starting with a semicolon would be
ignored by software. Since the only comment used was the first, it quickly became used to hold a
summary description of the sequence, often starting with a unique library accession number, and
with time it has become commonplace use to always use ">" for the first line and to not use ";"
comments (which would otherwise be ignored).
Following the initial line (used for a unique description of the sequence) is the actual sequence
itself in standard one-letter code. Anything other than a valid code would be ignored (including
spaces, tabulators, asterisks, etc...). Originally it was also common to end the sequence with an
"*" (asterisk) character (in analogy with use in PIR formatted sequences) and, for the same
reason, to leave a blank line between the description and the sequence.
A few sample sequences:
A multiple sequence FASTA format would be obtained by concatenating several single sequence
FASTA files. This does not imply a contradiction with the format as only the first line in a FASTA
file may start with a ";" or ">", hence forcing all subsequent sequences to start with a ">" in order
to be taken as different ones (and further forcing the exclusive reservation of ">" for the
sequence definition line). Thus, the examples above may as well be taken as a multisequence
file if taken together.
Description line[edit]
The description line (defline) or header line, which begins with '>', gives a name and/or a unique
identifier for the sequence, and may also contain additional information. In a deprecated practice,
the header line sometimes contained more than one header, separated by a ^A (Control-A)
character.
In the original Pearson FASTA format, one or more comments, distinguished by a semi-colon at
the beginning of the line, may occur after the header. Some databases and bioinformatics
applications do not recognize these comments and follow the NCBI FASTA specification. An
example of a multiple sequence FASTA file follows:
>SEQUENCE_1
MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG
LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK
IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL
MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL
>SEQUENCE_2
SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI
ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH
Sequence representation[edit]
After the header line and comments, one or more lines may follow describing the sequence:
each line of a sequence should have fewer than 80 characters. Sequences may be protein
sequences or nucleic acid sequences, and they can contain gaps or alignment characters
(see sequence alignment). Sequences are expected to be represented in the standard
IUB/IUPAC amino acid and nucleic acid codes, with these exceptions: lower-case letters are
accepted and are mapped into upper-case; a single hyphen or dash can be used to represent a
gap character; and in amino acid sequences, U and * are acceptable letters (see below).
Numerical digits are not allowed but are used in some databases to indicate the position in the
sequence.
The nucleic acid codes supported are:[1][2]
Meaning
Mnemonic
Adenine
Cytosine
Guanine
Thymine
Uracil
Meaning
Mnemonic
A or G
puRine
C, T or U
pYrimidines
G, T or U
A or C
C or G
Strong interaction
A, T or U
Weak interaction
not A (i.e. C, G, T or U)
B comes after A
not C (i.e. A, G, T or U)
D comes after C
not G (i.e., A, C, T or U)
H comes after G
V comes after U
ACGTU
Nucleic acid
The amino acid codes supported (25 amino acids and 3 special codes) are:
Meaning
Alanine
Meaning
Cysteine
Aspartic acid
Glutamic acid
Phenylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
Methionine
Asparagine
Pyrrolysine
Proline
Glutamine
Meaning
Arginine
Serine
Threonine
Selenocysteine
Valine
Tryptophan
Tyrosine
any
translation stop
Sequence identifiers[edit]
The NCBI defined a standard for the unique identifier used for the sequence (SeqID) in the
header line. The formatdb man page has this to say on the subject: "formatdb will automatically
parse the SeqID and create indexes, but the database identifiers in the FASTA definition line
must follow the conventions of the FASTA Defline Format."
The following list describes the NCBI FASTA defline format (see "The NCBI Handbook", Chapter
16, The BLAST Sequence Analysis Tool.).
Database
Format
GenBank
gb|accession|locus
emb|accession|locus
dbj|accession|locus
NBRF PIR
pir||entry
prf||name
SWISS-PROT
sp|accession|entry name
pdb|entry|chain
Patents
pat|country|number
GenInfo Backbone Id
bbs|number
gnl|database|identifier
ref|accession|locus
lcl|identifier
The vertical bars ("|") in the above list are not separators in the sense of the Backus-Naur form,
but are part of the format. Multiple identifiers can be concatenated, also separated by vertical
bars.
Compression[edit]
The compression of FASTA files requires a specific compressor to handle both channels of
information: identifiers and sequence. For improved compression results, these are mainly
divided in two streams where the compression is made assuming independence. For example,
the algorithm MFCompress [3] performs lossless compression of these files using context
modelling and arithmetic encoding.
File extension[edit]
There is no standard file extension for a text file containing FASTA formatted sequences. The
table below shows each extension and its respective meaning.
Extension
Meaning
Notes
fasta (.fas)
generic fasta
fna
ffn
FASTA nucleotide of
gene regions
faa
frn
FASTA non-coding
RNA
See also[edit]