---
name: "seqfmt"
section: "5"
platform: "linux"
package: "squizz"
version: "0.99d+dfsg-3"
release: "Debian 12 (Bookworm)"
platforms: ["linux"]
url: "https://new.carta.tech/seqfmt"
---

# seqfmt(5)

Sequences formats" 4

## NAME

seqfmt - Sequences formats" 4

## DESCRIPTION

This document illustrates some common formats used for sequences representation.

- **EMBL**

  ```
   ID   MMVASPHOS  standard; RNA; EST; 140 BP.
   AC   X97897;
   DE   M.musculus mRNA for protein homologous to
   DE   vasodilator-stimulated phosphoprotein
   SQ   Sequence 140 BP; 25 A; 58 C; 39 G; 17 T; 1 other;
        ttctcccaga agctgactct atggngaccc cgagagagac tgagcagaac      60
        ccccgcaccc ctgcacttcc aatcaggggc gccccgggag cactccccgt     120
        ccgccctccg cgcagccatg                                      140
   //
  ```

- **FASTA**

  ```
   >MMVASPHOS
   ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
   ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
   ccgccctccgcgcagccatg
  ```

- **GCG**

  ```
   !!NA_SEQUENCE 1.0
    (No documentation)
   dna1.txt  Length: 88  Nov 22, 2001 14:38  Type: N  Check: 3818  ..
          1  TAGTCGTAGT CGGAGCGATG CTGACGATGA CGATGACGAT CGTAGCTGAT
         51  CGATCGAGCT GATGCTGATC GAGCTAGCTG ATCGATCG
  ```

- **GDE**

  ```
   #sample1
   TTCAAGAGAAACAGCGGCCAAGGAAAAGACTCGGCATGATTGTCCATAGCTTACAAAGCG
   #sample2
   TTCAAGAGAAACAGCGGCTGGGGGAAAGACTCGTCCTGATTGCCTGTAGATGGTAAAGCG
  ```

- **GENBANK**

  ```
   LOCUS       HUMHBV1       130 bp    DNA         PRI     17-JUN-1993
   DEFINITION  Human DNA/endogenous Hepatitis B virus (HBV) DNA, left
               host viral junction.
   ACCESSION   M15770
   BASE COUNT       32 a     43 c     29 g     26 t
   ORIGIN
         1 agcgggcagt gcagctgctt ggacagcagg ggtgtttctt caacccaggc
        61 ctcctgtcac aacaggccca ttcaattctg aacctgcaag ccaactccaa
       121 cctcttttcc cagggggaac caaaaaccct
   //
  ```

- **IG**

  ```
   ; comment
   U03518
   AACCTGCGGAAGGATCATTACCGAGTGCGGGTCCTTTGGGCCCAACCTCCCATCCGTGTC
   TATTGTACCCTGTTGCTTCGGCGGGCCCGCCGCTTGTCGGCCGCCGGGGGGGCGCCTCTG
   TGAGTTGATTGAATGCAATCAGTTAAAACTTTCAACAATGGATCTCTTGGTTCCGGC1
  ```

- **NBRF** (pir)

  ```
   >P1;CCHU
   cytochrome c [validated] - human
   MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIW
   GEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE*
  ```

- **CODATA**

  ```
   ENTRY           CCHU  #type complete
   TITLE           cytochrome c [validated] - human
   ACCESSIONS      A31764; A05676; I55192; A00001
   SUMMARY         #length 105  #molecular-weight 11749  #checksum 3247
   SEQUENCE
                    5        10        15        20        25        30
          1 M G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G
         31 P N L H G L F G R K T G Q A P G Y S Y T A A N K N K G I I W
         61 G E D T L M E Y L E N P K K Y I P G T K M I F V G I K K K E
         91 E R A D L I A Y L K K A T N E
   ///
  ```

- **RAW**

  ```
   ttctcccagaagctgactctatggngaccccgagagagactgagcagaacctggagccag
   ccccgcacccctgcacttccaatcaggggcgccccgggagcactccccgtggcgcgccgc
   ccgccctccgcgcagccatg
  ```

  **Warning**: This format cannot handle more than one sequence per file.

- **SWISSPROT**

  ```
   ID   100K_RAT       STANDARD;      PRT;   149 AA.
   AC   Q62671;
   DE   100 kDa protein (EC 6.3.2.-).
   SQ   SEQUENCE   149 AA;  17004 MW;  D06484B8BC29112E CRC64;
        MMSARGDFLN YALSLMRSHN DEHSDVLPVL DVCSLKHVAY VFQALIYWIK
        PQLERKRTRE LLELGIDNED SEHENDDDTS QSATLNDKDD ESLPAETGQN
        SITIRPPDDQ HLPTANTCIS RLYVPLYSSK QILKQKLLLA IKTKNFGFV
   //
  ```

## SEE ALSO

- [**squizz**(1)](/squizz/1.md), [**alifmt**(5)](/alifmt/5.md)

  ## AUTHOR

Nicolas Joly (njoly@pasteur.fr), Institut Pasteur.