1. Sequence Formats
Suchat Udomsopagit

2. Sequences DNA and protein sequences
Can be read and written in a variety of formats
Sequence formats are ASCII TEXT
Required arrangement of characters, symbols and keywords that specify things
e.g. the sequence, ID name, comments, etc.
Program should look to find them in seq entry

3. Sequences
Never any hidden, unprintable 'control' characters in any sequence format.
All standard sequence formats can be printed out or viewed simply by displaying their file.

4. MS word Microsoft WORD format is not a sequence format.
If using a word-processor to type a sequence:
Save sequence to a file as ASCII text
Try selecting: File, Save As, Save as type Text
Do not using word-processors to write sequences
Simple text editors should be used:
Notepad
Wordpad
For UNIX
Pico
nedit

5. Some common formats Single sequence per file
Multiple sequences per file
Either single or multiple sequences per file
gcg
Multiple sequence format (msf)
fasta
staden
clustal
embl
phylip
Plus some others, e.g. MacVector, GeneWorks, DNA Strider etc.

6. Each Sequence analysis program has its own format for storing sequence data!!!

7. FASTA format First line is a Description line
A single-line
Contains a greater-than (">") symbol in the first column
Followed by lines of sequence data
It is recommended that all lines of text be shorter than 80 characters in length

8. FASTA format Description line
>gi|532319|pir|TVFV2E|TVFV2E envelope protein ELRLRYCAPAGFALLKCNDADYDGFKTNCSNVSVVHCTNLMNTTVTTGLLLNGSYSENRT QIWQKHRTSNDSALILLNKHYNLTVTCKRPGNKTVLPVTIMAGLVFHSQKYNLRLRQAWC HFPSNWKGAWKEVKEEIVNLPKERYRGTNDPKRIFFQRQWGDPETANLWFNCHGEFFYCK MDWFLNYLNNLTVDADHNECKNTSGTKSGNKRAPGPCVQRTYVACHIRSVIIWLETISKK TYAPPREGHLECTSTVTGMTVELNYIPKNRTNVTLSPQIESIWAAELDRYKLVEITPIGF APTEVRRYTGGHERQKRVPFVXXXXXXXXXXXXXXXXXXXXXXVQSQHLLAGILQQQKNL LAAVEAQQQMLKLTIWGVK
Sequence

9. Standard IUB/IUPAC amino acid and nucleic acid codes
Lower-case letters are accepted and are mapped into upper-case
No numerical digits in the sequence.
The nucleic acid codes supported are:
A  adenosine M  A C (amino)
C  cytidine S  G C (strong)
G  guanine W  A T (weak)
T  thymidine B  G T C
U  uridine D  G A T
R  G A (purine) H  A C T
Y  T C (pyrimidine) V  G C A
K  G T (keto) N  A G C T (any)
-  gap of indeterminate length

10. Standard IUB/IUPAC amino acid and nucleic acid codes
The accepted amino acid codes are:
A  alanine P  proline
B  aspartate or asparagine Q  glutamine
C  cystine R  arginine
D  aspartate S  serine
E  glutamate T  threonine
F  phenylalanine U  selenocysteine
G  glycine V  valine
H  histidine W  tryptophan
I  isoleucine Y  tyrosine
K  lysine Z  glutamate or glutamine
L  leucine X  any
M  methionine *  translation stop
N  asparagine -  gap of indeterminate length

11. FASTA format Multiple sequences Blank lines inserted > mysequence
ACGTCGATCGATCGATGCATCGTGCTAGCTACAGTCGATGCAT
CAGTCGATGCTAGCATGCTAGCTGCATCGATCGATGCTACGTA
CAGTCGATCGATGCAT
> mysequence2
ACCGTACGATGCTAGCTAGCTAGCTACAGTCAGTCGATGCTACG
CAGTCGTAGCATGCTAACGTCGATCGTA
> mysequence3
CAGTCAGTCGTAGCTAGCTAGCTAGCTAGGGGTATCGATGCTAA
CAGTACTTTGCATGCAGCATGCTAGCTAGCTAGCTA

12. Genbank File Format File Header
The first line in the file must have "GENETIC SEQUENCE DATA BANK" in spaces 20 through 46.
The next 8 lines may contain arbitrary text.
They are ignored but are required to maintain the GenBank format.

13. Genbank File Format Sequence Data Entries First line Second line
Begins with ‘LOCUS’ in the first 5 spaces
Followed by genetic locus name or identifier
Length of the sequences
Type of sequences
Second line
DEFINITION in the first 10 spaces
Followed by free form text to identify the sequence.
Third line
ACCESSION in the first 9 spaces
Spaces must hold the primary accession number
Fourth line
ORIGIN in the first 6 spaces
Nothing else is required on this line, it indicates that the nucleic acid sequence begins on the next line.

14. Genbank File Format Fifth line Last line
Begins the nucleotide sequence.
The first 9 spaces of each sequence line may either be blank or may contain the position in the sequence of the first nucleotide on the line.
The next 66 spaces hold the nucleotide sequence in six blocks of ten nucleotides.
Each of the six blocks begins with a blank space followed by ten nucleotides.
Thus the first nucleotide is in space 11 of the line while the last is in space 75.
Last line
Must have // in the first 2 spaces to indicate termination of the sequence.

15. Genbank File Format LOCUS name size bp type date dd-MON-yyyy
Genbank Locus name
total base count
DNA, RNA, PROTEIN, MASK, or TEXT
dd-MON-yyyy
LOCUS name size bp type date

16. Genbank Example LOCUS NM_079846 1190 bp mRNA linear INV 15-DEC-2001
DEFINITION Drosophila melanogaster Triose phosphate isomerase (Tpi), mRNA.
ACCESSION NM_079846
VERSION NM_ GI:
KEYWORDS .
SOURCE fruit fly.
ORGANISM Drosophila melanogaster
Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta;
Pterygota; Neoptera; Endopterygota; Diptera; Brachycera;
Muscomorpha; Ephydroidea; Drosophilidae; Drosophila.
REFERENCE 1 (bases 1 to 1190)
AUTHORS Shaw-Lee,R.L., Lissemore,J.L. and Sullivan,D.T.
TITLE Structure and expression of the triose phosphate isomerase (Tpi) gene of Drosophila melanogaster JOURNAL Mol. Gen. Genet. 230 (1-2), (1991)
MEDLINE
PUBMED
COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI
review. The reference sequence was derived from AE
FEATURES Location/Qualifiers
source
/organism="Drosophila melanogaster“
/db_xref="taxon:7227“
/chromosome="3“
/map="99E1-99E2“
gene
/gene="Tpi“
/note="TPI; TPIS; CG2171; CT6334“
/db_xref="FLYBASE:FBgn “
/db_xref="LocusID:43582“

17. Genbank Example CDS 181..924 /gene="Tpi“ /EC_number="5.3.1.1“
/note="Nucleotide sequence of the Celera sequence differs from the published
sequence for this transcript.“
/codon_start=1
/db_xref="FLYBASE:FBgn “
/db_xref="LocusID:43582“
/product="Triose phosphate isomerase“
/protein_id="NP_ “
/db_xref="GI: "
/translation="MSRKFCVGGNWKMNGDQKSIAEIAKTLSSAALDPNTEVVIGCPA IYLMYARNLLPCELGLAGQNAYKVAKGAFTGEISPAMLKDIGADWVILGHSERRAIFG ESDALIAEKAEHALAEGLKVIACIGETLEEREAGKTNEVVARQMCAYAQKIKDWKNVV VAYEPVWAIGTGQTATPDQAQEVHAFLRQWLSDNISKEVSASLRIQYGGSVTAANAKE LAKKPDIDGFLVGGASLKPEFVDIINARQ“
misc_feature
/note="TIM; Region: Triosephosphate isomerase“
BASE COUNT 279 a 368 c 323 g 220 t
ORIGIN
1 ttaatctcga atctgggaaa aatctgagtg gaaaagtcga cggcgagcct ccagtcatcg
61 agttacccac ttgaaattat cagttccaaa cactctaata gcagtcccct tgttttgtcc
121 cccgatccgc agttctacgc caatttcagc accgattgca ccgacagcaa cagcaacaac
181 atgagccgaa agttctgcgt gggaggcaac tggaagatga acggcgacca gaagtccatc
241 gccgagatcg ccaagaccct gagctcggcc gccctcgacc ccaacacgga ggtggtcatc
301 ggctgcccgg ccatctacct gatgtacgcc cgcaacctgc tgccctgcga gctgggtctg
361 gccggccaga atgcctacaa ggtggccaag ggcgcattca ccggcgagat ctcccctgcg
421 atgctgaagg //

18. EMBL File Format European Molecular Biology Laboratory First line
Begins with two letters ID
Followed by the EMBL identifier
Second line
AC, followed by accession number
Third line
DE, followed by a free form text definition
Fourth line
SQ, followed by the length of the sequence
After the sequence length there is a blank space and the two letters BP.

19. EMBL File Format Fifth line The last line ~ terminator line
Nucleotide sequence begins
Each line of sequence begins with four blank spaces
Next 66 spaces hold the nucleotide sequence in 6 blocks of 10 nucleotides.
Each of the six blocks begins with a blank space followed by ten nucleotides.
Thus the first nucleotide is in space 6 of the line while the last is in space 70.
The last line ~ terminator line
Two characters // in the first two spaces
Multiple sequences may appear in each file

20. EMBL Example (1) LINE 1 :ID ID_name LINE 2 :AC Accession number
LINE 3 :DE Describe the sequence any way you want
LINE 4 :SQ Length BP
LINE 5 : ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTA...
LINE 6 : ACGT...
LINE 7 ://

21. EMBL Example (2)

22. EMBL Example (3) ID DMTPIG standard; DNA; INV; 3419 BP. XX
AC X57576; S70377;
SV X
DT 20-JAN-1992 (Rel. 30, Created)
DT 19-AUG-1996 (Rel. 49, Last updated, Version 10)
DE D.melanogaster Tpi gene for Triosephosphate isomerase
KW glycolytic enzyme; tpi gene; triosephosphate isomerase.
OS Drosophila melanogaster (fruit fly)
OC Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila.
RN [1] RP
RA Sullivan D.T.;
RT ;
RL Submitted (07-FEB-1991) to the EMBL/GenBank/DDBJ databases.
RL D.T. Sullivan, Biological Research Laboratories, 130 College Pl, Syracuse
RL University, Syracuse, NY 13244, USA

23. RN [3]
RX MEDLINE;
RA Shaw-Lee R.L., Lissemore J.L., Sullivan D.T.;
RT "Structure and expression of the triose phosphate isomerase (Tpi) gene of
RT Drosophila melanogaster.";
RL Mol. Gen. Genet. 230: (1991). XX
DR FLYBASE; FBgn ; Tpi.
DR SWISS-PROT; P29613; TPIS_DROME.
FH Key Location/Qualifiers FH
FT source
FT /db_xref="taxon:7227"
FT /germline
FT /organism="Drosophila melanogaster"
FT /strain="Oregon-R"
FT /clone_lib="EMBL-4"
FT CDS join( , )
FT /db_xref="FLYBASE:FBgn "
FT /db_xref="SWISS-PROT:P29613"
FT /gene="Tpi"
FT /EC_number=" "
FT /product="triosephosphate isomerase"
FT /protein_id="CAA "
FT /translation="MSRKFCVGGNWKMNGDQKSIAEIAKTLSSAALDPNTEVVIGCPAI
FT YLMYARNLLPCELGLAGQNAYKVAKGAFTGEISPAMLKDIGADWVILGHSERRAIFGES
FT DALIAEKAEHALAEGLKVIACIGETLEEREAGKTNEVVARQMCAYAQKIKDWKNVVVAY
FT EPVWAIGTGKTATPDQAQEVHASLRQWLSDNISKEVSASLRIQYGGSVTAANAKELAKK
FT PDIDGFLVGGASLKPEFLDIINARQ"
FT mRNA join( , , )
FT prim_transcript

24. FT exon
FT /number=1
FT exon
FT /number=2
FT exon
FT /number=3
FT intron
FT intron
FT misc_feature
FT /note="intron 1 lariat sequence"
FT misc_feature
FT /note="intron 2 lariat sequence"
FT polyA_signal XX
SQ Sequence 3419 BP; 855 A; 933 C; 849 G; 778 T; 4 other;
gatctcgagc gagaaatgtg gaacatagtg gaggcctcca gtggcgccga gctgggtgaa
accagctacg agttcccttc ccccgctccg gttcccagcg cagcagtgaa cgaaatagca
gttccacagt cccaccagct cctcctgctc ctgcgaagcc ctcagttccg tccgcctcct
atgacaacca caactacagt ttcagccagg atgaggacga agatgatgat gatctggagt
ttgaggacgt attcgtgccg gccagctctg ttccaaatcc cgttcagcct ggcatagatc
ccgtggaact gcgtcgctcc ctggctttgg tcatgaggga gaaattgcga tcggatgaca
cggactccag gccaatgggc aacaatcagg atcttcccat agatgaacag tccagggaga
gaccgctctc cactcaaaca tctcccacaa atggcccact tccggctctt ctgagggcca
aactgcttgc tgggcaactc nnnncaatag cgctcactgc ctgccaggat ccacggcgag
tcctgctccc caggagcaat ccggtatctt tgtgatcgat agtgaggcga gtcccggctc
aaatgggcac aagcctaagt atcgaaaggg cacggcattc actcggagtt cgctgaagaa
gagccgatcc tgcaactgta gctccatcgc taagggacga ggggtccacg acgagcccag
cagtaatctc tgcagggatc aggagtcctc tgtacttcca cagcatccgc agccagccaa
ccatcccaca gagaactttt //

25. National Biomedical Research Foundation (NBRF) format Protein Information Resource (PIR) format
First line
Begins with a greater than symbol (>)
Immediately followed by 2 character sequence type specifier
Specifier Sequence type
P protein, complete
F protein, fragment
DL DNA, linear
DC DNA, circular
RL RNA, linear
RC RNA, circular
N functional RNA, other than tRNA
N tRNA
Then a semicolon (;)
Followed by sequence name or identification code for the NBRF database
Four to six letters and numbers
>P1;CBRT

26. Second line contains two kinds of information
National Biomedical Research Foundation (NBRF) format Protein Information Resource (PIR) format
Second line contains two kinds of information
First:
Sequence name
Followed by 3 characters blank space, " - “
Second
Organism or organelle name
>P1;CBRT
Cytochrome b - Rat mitochondrion (SGC1)

27. Amino acid or nucleic acid sequence begins on line three
National Biomedical Research Foundation (NBRF) format Protein Information Resource (PIR) format
Amino acid or nucleic acid sequence begins on line three
Free format
May be interrupted by blanks for ease of reading
Protein sequences
May contain special punctuation to indicate various indeterminacies in the sequence
The last character in the sequence must be an asterisks (*).

28. NBRF/PIR Example LINE 1 :>P1;CBRT
LINE 2 :Cytochrome b - Rat mitochondrion (SGC1)
LINE 3 :M T N I R K S H P L F K I I N H S F I D L P A P S
LINE 4 : VTHICRDVN Y GWL IRY
LINE 5 :TWIGGQPVEHPFIIIGQLASISYFSIILILMPISGIVEDKMLKWN*

29. MolGen/Stanford File Format
Molecular Genetics Group at Stanford U.
First line ~ comment line
Begins with a semi-colon (;)
Followed by descriptive text
May be as many comment lines as desired
Need not be present
Second line
Must be present
Contains an identifier or name for the sequence

30. MolGen/Stanford File Format
Third line
Sequence begins
Occupies up to 80 spaces
Spaces may be included in the sequence for ease of reading.
Terminated with 1 or 2
1 indicates a linear sequence
2 marks a circular sequence

31. MolGen/Stanford Example
LINE 1 :; Describe the sequence any way you want
LINE 2 :ECTRNAGLY2
LINE 3 :ACGCACGTAC ACGTACGTAC A C G T C C G T ACG TAC GTA CGT
LINE 4 : GCTTA GG G C T A1

32. PHYLIP File Format Interleaved and Sequential formats
Created and used by several phylogenetics programs

33. PHYLIP File Format Interleaved format
a MNTTNCFIAL VHAIREIRAF FLSRATG-KM EFTLYNGERK TFYSRPNNHD
a MNTTDCFIAL VTAIREIRAF FLPRATG-RM EFTLHNGERK VFYSRPNNHD
c-s8c1 MNTTDCFIAV VNAIKEVRAL FLPRTAG-KM EFTLHDGEKK VFYSRPNNHD
c1nov MNTTDCFIAV VNAIREIRAL FLPRTTG-KM EFTLHDGEKK VFYSRPNNHD
o1brazl MNTTDCFIAL VQAIREIKAL FLPRTTG-KM ELTLYNGEKK TFYSRPNNHD
o1campos MNTTDCFIAL VQAIREIKAL FLPRTTG-KM ELTLYNGEKK TFYSRPNNHD
o1kauf MNTTDCFIAL VQAIREIKAL FLSRTTG-KM ELTLYNGEKK TFYSRPNNHD
ken MNTTDCFIAL LRAFREIKTL FLSRVRG-KM EFTLYNGEKK TFYSRPNNHD
ken MNTTDCFIAL VRAIREFKIL FSLRPLARKM EFTLYNGIKK TFYSRPNKHD
ken MNTTDCFIAL VQAIREIKLL FKG--IR-KM KLTLYNGEKK TFYSRPNSHD
uga MNTTDCFIAL VQAIREIKSL FRS--SR-KM EFTLYNGEKK TFYSRPNNHD
bec MKTTDCFNVL FEIFHRFGQT FKA--DR-KM EFTLYNGEKK TFYSRPNTHG
zim MKTTDCFDVL LEIFHRFRQT FKT--DR-KM EFTLYNGEKK TFYSRPNTHG
knp MKTTDCFNVL LETFHRFRNV FKT--DR-KM EFTLYNGDKK TFYSRPNTHG
zim MKTTGCFDVL IEIAHRLRQL NKT--DR-KM EFTLYNGEKK TFYSRPNTHG
zim MKTTDCFNVL LEIIYRFRHT FKT--DR-KM EFTLYNGEKK TFYSRPNKHG
knp MKTTDCFSVL FEIFHRLRHT LKT--ER-KM EFTLYNGERK TFYSRPNKHG
zam MKTTDCFDAL LEAFHRLRQT FKT--DR-KM EFTLYNGEKK TFYSRPNRHG
NCWLNTILQL FRYVDEPFFD WVYNSPENLT LAAIKQLEEL TGLELHEGGP
NCWLNTILQL FRYVGEPFFD WVYDSPENLT LEAIEQLEEL TGLELHEGGP
NCWLNTILQL FRYVDEPFFD WVYNSPENLT LEAIKQLEEL TGLELREGGP
NCWLNAILQL FRYVEEPFFD WVYSTPENLT LEAIKQLEDL TGLELHEGGP
NCWLNAILQL FRYVEEPFFD WVYSSPENLT LEAIKQLEDL TGLELHEGGP
NCWLNAILQL FRYVDEPFFE WVYDSPENLT VEAIRQLEEL TGLELHEGGP
NCWLNAILQL FRYVDEPFFD WVYESPENLT IQAIGQLEEL TGLDLREGGP
NCWLNTILQL FRYVDEPFFD WVYNSPENLT LRAIEQLEEL TGLELREGGP
NCWLNTILQL FRYVDEPFFD WVYNSPENLT LQAIEQLEEL TGLELHEGGP
NCWLNSLLQL FRYVDEPLFE SEYLSPENKT LDMIKQLSDY TKLDLSDGGP
NCWLNSLLQL FRYVDEPLFE SEYLSPENKT LDMIKRLSDY TKLDLSDGGP
PALVIWNIKH LLQTGIGTAS RPAR-CMVDG TNMCLADFHA GIFLKEQEHA
PALVIWNIKH LLHTGIGTAS RPSEVCMVDG TNMCLADFHA GIFLKGQEHA
PALVIWNIKH LLHTGIGTAS RPSEVCMVDG TDMCLADFHA GIFMKGREHA
PALVIWNIKH LLHTGIGTAS RPSEVCMVDG TDMCLADFHA GIFMKGQEHA
PALVIWNIKH LLHTGIGTAS RPSEVCMVDG TDMCLADFHA GIFLKGQEHA …
Interleaved format
Similar to the output of alignment programs
The first part of file contains the first part of each of the sequences
Only the first parts of the sequences should be preceded by names
Then the second part of each sequence, and so on.

34. PHYLIP File Format Sequential format
All of one sequence is given, possibly on multiple lines, before the next starts. YF
a MNTTNCFIAL VHAIREIRAF FLSRATG-KM EFTLYNGERK TFYSRPNNHD
NCWLNTILQL FRYVDEPFFD WVYNSPENLT LAAIKQLEEL TGLELHEGGP
PALVIWNIKH LLQTGIGTAS RPAR-CMVDG TNMCLADFHA GIFLKEQEHA
VFACVTSNGW YAIDDEDFYP WTPDPSDVLV FVPYDQEPLN GGWKANVQRK
LK----
a MNTTDCFIAL VTAIREIRAF FLPRATG-RM EFTLHNGERK VFYSRPNNHD
NCWLNTILQL FRYVGEPFFD WVYDSPENLT LEAIEQLEEL TGLELHEGGP
PALVIWNIKH LLHTGIGTAS RPSEVCMVDG TNMCLADFHA GIFLKGQEHA
VFACVTSNGW YAIDDDDFYP WTPDPSDVLV FVPYDQEPLN GEWKTKVQQK
c-s8c MNTTDCFIAV VNAIKEVRAL FLPRTAG-KM EFTLHDGEKK VFYSRPNNHD
NCWLNTILQL FRYVDEPFFD WVYNSPENLT LEAIKQLEEL TGLELREGGP
PALVIWNIKH LLHTGIGTAS RPSEVCMVDG TDMCLADFHA GIFMKGREHA
VFACVTSNGW YAIDDEDFYP WTPDPSDVLV FVPYDQEPLN EGWKASVQRK
LKGAGQ
c1nov MNTTDCFIAV VNAIREIRAL FLPRTTG-KM EFTLHDGEKK VFYSRPNNHD
PALVIWNIKH LLHTGIGTAS RPSEVCMVDG TDMCLADFHA GIFMKGQEHA
VFACVTSNGW YAIDDEDFYP WTPDPSDVLV FVPYDQEPLN EGWKANVQRK
o1brazl MNTTDCFIAL VQAIREIKAL FLPRTTG-KM ELTLYNGEKK TFYSRPNNHD
NCWLNAILQL FRYVEEPFFD WVYSTPENLT LEAIKQLEDL TGLELHEGGP
PALVIWNIKH LLHTGIGTAS RPSEVCMVDG TDMCLADFHA GIFLKGQEHA
VFACVTSNGW YAIDDEDFYP WTPDPSDVLV FVPYDQEPLN GEWKAKVQRK
o1campos MNTTDCFIAL VQAIREIKAL FLPRTTG-KM ELTLYNGEKK TFYSRPNNHD
VFAC…

35. Protein Data Bank (PDB) File Format
Each line is 80 columns wide and is terminated by an end-of-line indicator.
The first 6 columns of every line contain a "record name".
The list of ATOM records in each polymer chain must be terminated by a TER record.
ATOM records for polymer atoms must include non-blank chain ID fields.
To use the automatic validation check, the coordinate file must include a complete CRYST1 record defining the unit cell and space group information.
Each file should terminate with a line containing only the word END.

36. Protein Data Bank (PDB) File Format
COLUMNS DATA TYPE FIELD DEFINITION
Record name "ATOM "
Integer serial Atom serial number.
Atom name Atom name.
Character altLoc Alternate location indicator.
Residue name resName Residue name.
Character chainID Chain identifier.
Integer resSeq Residue sequence number.
AChar iCode Code for insertion of residues.
Real(8.3) x Orthogonal coordinates for X in
Angstroms.
Real(8.3) y Orthogonal coordinates for Y in
Real(8.3) z Orthogonal coordinates for Z in
Real(6.2) occupancy Occupancy.
Real(6.2) tempFactor Temperature factor.
LString(4) segID Segment identifier, left-justified.
LString(2) element Element symbol, right-justified.
LString(2) charge Charge on the atom.

37. Protein Data Bank (PDB) File Format
Pattern:
RTyp Num Atm Res Ch ResN X Y Z Occ Temp PDB Line
ATOM N ASP L FDL 93
ATOM CA ASP L FDL 94
Where:
RTyp: Record Type
Num: Serial number of the atom. Each atom has a unique serial number.
Atm: Atom name (IUPAC format).
Res: Residue name (IUPAC format).
Ch: Chain to which the atom belongs (in this case, L for light chain of an antibody).
ResN: Residue sequence number.
X, Y, Z: Cartesian coordinates specifying atomic position in space.
Occ: Occupancy factor
Temp: Temperature factor (atoms disordered in the crystal have high temperature factors).
PDB: The PDB data file unique identifier.
Line: Line (record) number in the data file.

38. PDB Example
HEADER LYASE JUL QU TITLE CRYSTAL STRUCTURE OF TRYPANOSOMA BRUCEI ORNITHINE TITLE 2 DECARBOXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORNITHINE DECARBOXYLASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: ; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 4 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 5 EXPRESSION_SYSTEM_STRAIN: B21/DG3; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS POLYAMINE METABOLISM, PYRIDOXAL 5'-PHOSPHATE, ALPHA-BETA KEYWDS 2 BARREL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR N.V.GRISHIN,A.L.OSTERMAN,H.B.BROOKS,M.A.PHILLIPS, AUTHOR 2 E.J.GOLDSMITH REVDAT DEC-99 1QU JRNL COMPND REMARK REVDAT NOV-99 1QU JRNL AUTH N.V.GRISHIN,A.L.OSTERMAN,H.B.BROOKS,M.A.PHILLIPS, JRNL AUTH 2 E.J.GOLDSMITH JRNL TITL X-RAY STRUCTURE OF ORNITHINE DECARBOXYLASE FROM JRNL TITL 2 TRYPANOSOMA BRUCEI: THE NATIVE STRUCTURE AND THE JRNL TITL 3 STRUCTURE IN COMPLEX WITH JRNL TITL 4 ALPHA-DIFLUOROMETHYLORNITHINE JRNL REF BIOCHEMISTRY V JRNL REFN ASTM BICHAW US ISSN REMARK REMARK REMARK 2 RESOLUTION ANGSTROMS.
REMARK …

39. DBREF 1QU4 A SWS P DCOR_TRYBB DBREF 1QU4 B SWS P DCOR_TRYBB DBREF 1QU4 C SWS P DCOR_TRYBB DBREF 1QU4 D SWS P DCOR_TRYBB SEQRES 1 A GLY ALA MET ASP ILE VAL VAL ASN ASP ASP LEU SER CYS SEQRES 2 A ARG PHE LEU GLU GLY PHE ASN THR ARG ASP ALA LEU CYS SEQRES 3 A LYS LYS ILE SER MET ASN THR CYS ASP GLU GLY ASP PRO SEQRES 4 A PHE PHE VAL ALA ASP LEU GLY ASP ILE VAL ARG LYS HIS SEQRES 5 A GLU THR TRP LYS LYS CYS LEU PRO ARG VAL THR PRO PHE SEQRES 6 A TYR ALA VAL LYS CYS ASN ASP ASP TRP ARG VAL LEU GLY SEQRES 7 A THR LEU ALA ALA LEU GLY THR GLY PHE ASP CYS ALA SER SEQRES 8 A ASN THR GLU ILE GLN ARG VAL ARG GLY ILE GLY VAL PRO SEQRES 9 A PRO GLU LYS ILE ILE TYR ALA ASN PRO CYS LYS GLN ILE SEQRES 10 A SER HIS ILE ARG TYR ALA ARG ASP SER GLY VAL ASP VAL SEQRES 11 A MET THR PHE ASP CYS VAL ASP GLU LEU GLU LYS VAL ALA SEQRES 12 A LYS THR HIS PRO LYS ALA LYS MET VAL LEU ARG ILE SER SEQRES 13 A THR ASP ASP SER LEU ALA ARG CYS ARG LEU SER VAL LYS SEQRES 14 A PHE GLY ALA LYS VAL GLU ASP CYS ARG PHE ILE LEU GLU SEQRES 15 A GLN ALA LYS LYS LEU ASN ILE ASP VAL THR GLY VAL SER SEQRES 16 A PHE HIS VAL GLY SER GLY SER THR ASP ALA SER THR PHE SEQRES 17 A ALA GLN ALA ILE SER ASP SER ARG PHE VAL PHE ASP MET SEQRES 18 A GLY THR GLU LEU GLY PHE ASN MET HIS ILE LEU ASP ILE SEQRES 19 A GLY GLY GLY PHE PRO GLY THR ARG ASP ALA PRO LEU LYS SEQRES 20 A PHE GLU GLU ILE ALA GLY VAL ILE ASN ASN ALA LEU GLU SEQRES 21 A LYS HIS PHE PRO PRO ASP LEU LYS LEU THR ILE VAL ALA SEQRES 22 A GLU PRO GLY ARG TYR TYR VAL ALA SER ALA PHE THR LEU SEQRES 23 A ALA VAL ASN VAL ILE ALA LYS LYS VAL THR PRO GLY VAL SEQRES 24 A GLN THR ASP VAL GLY ALA HIS ALA GLU SER ASN ALA GLN SEQRES 25 A SER PHE MET TYR TYR VAL ASN ASP GLY VAL TYR GLY SER SEQRES 26 A PHE ASN CYS ILE LEU TYR ASP HIS ALA VAL VAL ARG PRO SEQRES 27 A LEU PRO GLN ARG GLU PRO ILE PRO ASN GLU LYS LEU TYR SEQRES 28 A PRO SER SER VAL TRP GLY PRO THR CYS ASP GLY LEU ASP SEQRES 29 A GLN ILE VAL GLU ARG TYR TYR LEU PRO GLU MET GLN VAL SEQRES 30 A GLY GLU TRP LEU LEU PHE GLU ASP MET GLY ALA TYR THR SEQRES 31 A VAL VAL GLY THR SER SER PHE ASN GLY PHE GLN SER PRO SEQRES 32 A THR ILE TYR TYR VAL VAL SER GLY LEU PRO ASP HIS VAL SEQRES 33 A VAL ARG GLU LEU LYS SER GLN LYS SER

40. HET PLP A HET PLP B HET PLP C HET PLP D HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 COMPLEX FORMUL 5 PLP 4(C8 H10 N1 O6 P1) HELIX LEU A LEU A HELIX LYS A ASN A HELIX ASP A GLY A HELIX SER A ILE A HELIX PRO A GLU A HELIX GLN A SER A HELIX CYS A HIS A HELIX LYS A GLU A HELIX ASP A LEU A HELIX ALA A LEU A HELIX LYS A PHE A HELIX GLY A ALA A HELIX PHE A HIS A HELIX THR A THR A HELIX SER A PHE A SHEET A 6 GLN A 365 PRO A SHEET A 6 LEU A 350 TRP A N TYR A O LEU A SHEET A 6 SER A 313 VAL A O PHE A N SER A SHEET A 6 PHE A 284 THR A N ILE A O TYR A SHEET A 6 PHE A 40 ASP A O PHE A N ALA A SHEET A 6 THR A 404 VAL A O THR A N PHE A SHEET A1 6 GLN A 365 PRO A SHEET A1 6 LEU A 350 TRP A N TYR A O LEU A SHEET A1 6 SER A 313 VAL A O PHE A N SER A SHEET A1 6 PHE A 284 THR A N ILE A O TYR A SHEET A1 6 TRP A 380 PHE A N LEU A O VAL A SHEET A1 6 PRO A 338 PRO A O LEU A N LEU A 382

41. CRYST P ORIGX ORIGX ORIGX SCALE SCALE SCALE ATOM N ASP A N ATOM CA ASP A C ATOM C ASP A C ATOM O ASP A O ATOM CB ASP A C ATOM CG ASP A C ATOM OD1 ASP A O ATOM OD2 ASP A O ATOM N GLU A N ATOM CA GLU A C ATOM C GLU A C ATOM O GLU A O ATOM CB GLU A C ATOM CG GLU A C ATOM CD GLU A C ATOM OE1 GLU A O ATOM OE2 GLU A O ATOM N GLY A N ATOM CA GLY A C ATOM C GLY A C ATOM O GLY A O ATOM N ASP A N ATOM CA ASP A C ATOM C ASP A C ATOM O ASP A O ATOM CB ASP A C ATOM CG ASP A C ATOM OD1 ASP A O ATOM CA PHE A C ...
CONECT CONECT MASTER END

42. Conversion of Sequence Formats
readseq (all flavors of UNIX)
1. IG/Stanford 10. Olsen (in-only)
2. GenBank/GB 11. Phylip3.2 (Sequential)
3. NBRF 12. Phylip (Interleaved)
4. EMBL 13. Plain/Raw
5. GCG 14. PIR/CODATA
6. DNAStrider 15. MSF
7. Fitch 16. ASN.1
8. Pearson/Fasta 17. PAUP/NEXUS
9. Zuker (in-only) 18. Pretty (out-only)

43. Conversion of Sequence Formats
seqret (EMBOSS)
gcg GCG 9.x and 10.x format
embl
swiss
fasta
genbank
nbrf
pir NBRF (PIR)
codata CODATA format.
strider DNA strider format
clustal
phylip PHYLIP non-interleaved multiple alignment format.
acedb ACeDB format
msf Wisconsin Package GCG's MSF multiple sequence format.
hennig86 Hennig86 format
jackknifer Jackknifer format
jackknifernon Jackknifernon format
nexus
paup Nexus/PAUP format
treecon Treecon format
mega Mega format
ig IntelliGenetics format.
staden
text

44. Conversion of Sequence Formats
Using Perl
Downloadable from Biomolecular Engineering Research Center (BMERC)
pdb-to-seq.pl: pdb  several standard formats
fa2tbl.pl: fasta  sequence table (.tbl) file
tbl2fa.pl: .tbl file  fasta
etc.

45. Conversion of Sequence Formats
Web-based
WWW READSEQ Sequence Conversion at NIH
WWW READSEQ at Human Genome Mapping Project (HGMP) Center

47. Conversion of Sequence Formats
Biological software at Institut Pasteur
READSEQ
EMBOSS
Abiview: trace files (ABI)  fasta
EMBOSS:
cutseq: Removes a specified section from a sequence
pasteseq: Insert one sequence into another.
nthseq: Writes one sequence from a multiple set of sequences.
extractseq: Extract regions from a sequence.

48. Conversion of Sequence Formats
Windows-based program
SeqVerter
Downloadable from GeneStudio, Inc. (free)
Read: ABI traces, Clustal, DCSE, DNASIS, DNAStar, DNAStrider (including binary), EMBL, FASTA, GDE, GenBank, IBI/Pustell, Macaw, MSF, Nexus/PAUP, PHYLIP Interleaved, PIR/NBRF, SCF 2.0 and SCF 3.0 traces, Swiss-Prot, and TreeCon.
Write: Clustal, DNASIS, DNAStar, FASTA and FASTA-SequIn, GenBank, IBI/Pustell, MSF, Nexus/PAUP, PHYLIP Interleaved, and TreeCon.
Tutorial also available

49. Reference Fundamentals of Sequence Analysis. (ppt)
Fourie Joubert. Bioinformatics Training at SANBI, 2001
EMBOSS Sequence Formats
Exchanging Sequence Data
Sequence Analysis Tools
Sequence Formats
Sequence file formats
Mount, DW. (2001) Bioinformatics: Sequence and Genome Analysis. Chapter 2: Collecting and Storing Sequences in the Laboratory. Cold Spring Harbor Laboratory Press. NY. pp