biology

Stockholm format

Stockholm format is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Stockholm format rather than just read about it. In short: Stockholm format is a multiple sequence alignment format used by Pfam, Rfam and Dfam, to disseminate protein, RNA and DNA sequence alignments. The alignment editors Ralee, Belvu and Jalview support Stockholm format as do the probabilistic database search tools, Infernal and HMMER, and the phylogenetic analysis tool Xrate.

Key takeaways

Stockholm format belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Stockholm format to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Stockholm format from memory before moving on to harder problems.

Reference excerpt

Stockholm format is a multiple sequence alignment format used by Pfam, Rfam and Dfam, to disseminate protein, RNA and DNA sequence alignments. The alignment editors Ralee, Belvu and Jalview support Stockholm format as do the probabilistic database search tools, Infernal and HMMER, and the phylogenetic analysis tool Xrate. Stockholm format files often have the filename extension .sto or .stk.

Syntax A well-formed stockholm file always contains a header which states the format and version identifier, currently '# STOCKHOLM 1.0'. The header is then followed by a multiple lines, a mix of markup (starting with #) and sequences. Finally, the "//" line indicates the end of the alignment. An example without markup looks like:

# STOCKHOLM 1.0 #=GF ID EXAMPLE <seqname> <aligned sequence> <seqname> <aligned sequence> <seqname> <aligned sequence> //

Sequences are written one per line. The sequence name is written first, and after any number of whitespaces the sequence is written. Sequence names are typically in the form "name/start-end" or just "name". Sequence letters may include any characters except whitespace. Gaps may be indicated by "." or "-". Mark-up lines start with #. The "parameters" are separated by whitespace, so an underscore ("_") instead of space should be used for the 1-char-per-column markups. Mark-up types defined include:

#=GF <feature> <Generic per-File annotation, free text> #=GC <feature> <Generic per-Column annotation, exactly 1 char per column> #=GS <seqname> <feature> <Generic per-Sequence annotation, free text> #=GR <seqname> <feature> <Generic per-Residue annotation, exactly 1 char per residue>

Recommended features These feature names are used by Pfam and Rfam for specific types of annotation. (See the Pfam and the Rfam documentation under "Description of fields")

#=GF Pfam and Rfam may use the following tags:

Compulsory fields: ------------------ AC Accession number: Accession number in form PFxxxxx (Pfam) or RFxxxxx (Rfam). ID Identification: One word name for family. DE Definition: Short description of family. AU Author: Authors of the entry. SE Source of seed: The source suggesting the seed members belong to one family. SS Source of structure: The source (prediction or publication) of the consensus RNA secondary structure used by Rfam. BM Build method: Command line used to generate the model SM Search method: Command line used to perform the search GA Gathering threshold: Search threshold to build the full alignment. TC Trusted Cutoff: Lowest sequence score (and domain score for Pfam) of match in the full alignment. NC Noise Cutoff: Highest sequence score (and domain score for Pfam) of match not in full alignment. TP Type: Type of family -- presently Family, Domain, Motif or Repeat for Pfam. -- a tree with roots Gene, Intron or Cis-reg for Rfam. SQ Sequence: Number of sequences in alignment.

Optional fields: ---------------- DC Database Comment: Comment about database reference. DR Database Reference: Reference to external database. RC Reference Comment: Comment about literature reference. RN Reference Number: Reference Number. RM Reference Medline: Eight digit medline UI number. RT Reference Title: Reference Title. RA Reference Author: Reference Author RL Reference Location: Journal location. PI Previous identifier: Record of all previous ID lines. KW Keywords: Keywords. CC Comment: Comments. NE Pfam accession: Indicates a nested domain. NL Location: Location of nested domains - sequence ID, start and end of insert. WK Wikipedia link: Wikipedia page CL Clan: Clan accession MB Membership: Used for listing Clan membership

For embedding trees: ---------------- NH New Hampshire A tree in New Hampshire eXtended format. TN Tree ID A unique identifier for the next tree.

Other: ------ FR False discovery Rate: A method used to set the bit score threshold based on the ratio of expected false positives to true positives. Floating point number between 0 and 1. CB Calibration method: Command line used to calibrate the model (Rfam only, release 12.0 and later)

Notes: A tree may be stored on multiple #=GF NH lines. If multiple trees are stored in the same file, each tree must be preceded by a #=GF TN line with a unique tree identifier. If only one tree is included, the #=GF TN line may be omitted.

#=GS Rfam and Pfam may use these features:

Feature Description --------------------- ----------- AC <accession> ACcession number DE <freetext> DEscription DR <db>; <accession>; Database Reference OS <organism> Organism (species) OC <clade> Organism Classification (clade, etc.) LO <look> Look (Color, etc.)

… excerpt ends here. Continue reading the full article.

Worked examples

Example 1 — a first encounter with Stockholm format

Start with the simplest possible case. Write down what Stockholm format claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Stockholm format before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Stockholm format ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Stockholm format

In research: Stockholm format appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Stockholm format in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Stockholm format is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics, Biological sequence format, so understanding it makes those chapters shorter.
In everyday life: Look for Stockholm format outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Stockholm format in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Stockholm format means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Stockholm format out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Stockholm format in simple terms?

Why does Stockholm format matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Stockholm format?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Stockholm format.