Inspired by Keith Robison's post on "cheat sheets", what would you put on a cheat sheet for bioinformatics? This might include one-line scripts, conversion factors, handy rules of thumb, etc.

Some of Keith's suggestions, which have a biology slant:

• IUPAC ambiguity codes for nucleotides:
• Amino acid single letter codes.
• SI prefixes in order.
• Powers of 2.
• Tm calculation estimation using G+C and A+T counts.
• 1 human genome ~= 7 pg of DNA
• 1 bp = 660 daltons

• 5' : left
• 3' : right

[?]

Not completely bioinformatics oriented, but some things I've found handy.

#subtract a small file from a bigger file
grep -vf filesmall filebig

#use awk to rearrange columns
awk '{print $2 " " $1}' file.txt

#sort a bed file by chrom, position
sort -k1,1 -k2,2n file.bed > file.sort.bed

#strip header
tail +2 file > file.nh

#find and replace over multiple files
perl -pi -w -e 's/255,165,0/255,69,0/g' *.wig

#print line 83 from a file
sed -n '83p'

#insert a header line
sed -i -e '1itrack name=test type=bedGraph' file.bed

#sum column one from a file
awk '{s+=$1} END {print s}' mydatafile

I have a vision of this cheat sheet being an extensive, very convenient set of environment variables and man pages. It should be versioned and should be on something like GitHub.

For example:

####################
# HG19
####################
$CHR1_SIZE=249250621
$CHR2_SIZE=243199373
...

####################
# Shortcuts
####################
$SUMCOL='awk '\''{ SUM += $1} END { print SUM}'\'

Other informational stats should be rolled into "man" entries. For example,

man dna
man iupac
man 2_powers
man log_examples

This may be utterly harebrained, but it seems useful to me. A community-based, focused wikipedia and shortcut library on the command line.

missing from the list

• 1 nucleosome = 147bp
• Crude AA to kilo dalton conversion = AA No X 0.11 =Kd
• Perl one liners for text conversion
• s/015012/012/ # Windows -> Unix
• s/012/015012/ # Unix -> Windows

This reminds me a little bit of BioNumbers: http://bionumbers.hms.harvard.edu

My cheat sheet would contain the length of the human chromosomes.

• AUG = Initiation

• UAA, UGA, UAG= Termination

• AT= 2 Hydrogen Bond, GC =3 Hygrogen Bond and adjacent bases are separated by 3.4Å

• Purine= Adenine & Guanine AND Pyrimidines= Cytosine, Uracil & Thymine

• DNA replication is semi-conservative

Coming more.... :D

The cheat sheet for programming in R would be what you are looking for.

Here are good manuals that my advisor, Thomas Girke, wrote:

• R & Bioconductor Manual
• HT Sequence Analysis with R and Bioconductor

The HT Sequence Analysis manual was as recommended in http://biostar.stackexchange.com/questions/539/recommend-your-favorite-introductory-r-in-bioinformatics-books-and-resources

Correspondance between the genome version nomenclature : [?]hg19 (UCSC) = GRCh37 (NCBI)[?]

I'll start off with a few of my own:

• an alpha-helix has 3.6 residues per turn

• A haploid human genome has a little over 3 billion bases and contains around 20,000 genes

• A handy alias for summing up a column of numbers from the command line:

  sumcol='awk '\''{ SUM += $1} END { print SUM}'\'

I would like a cheat sheet of arguments for common bioinformatics executables (e.g. blast, clustal, bowtie, bwa, fastx-toolkit), the popular bioperl scripts (like bp_seqfeature_load.pl), as well as the most common bioinformatics things in bash (e.g. mass renaming: foreach f in *fasta; do mv $f echo $f | sed -e 's/.fasta/.fa'; done)

building up my list here.. a blog post would be a good record for myself when i change computers or move office where i usually lose my printed copies.

http://kevin-gattaca.blogspot.com/2011/03/cheat-sheets-galore-bioinformatics.html

Very cool question, here's mine, which probably isn't all that relevant to most biostar members but is popular in our lab:

A table of nucleotide substitution models, and how to set them in the most commonly used programs

Still working on it (you can implement the exotic models in most of the software, but not easily)

My cheat sheet would be

Amino acid structures with their properties

And I would also consider Biostar because it is in fact more than google.

Great ideas! I'd add a Blosum62 substitution matrix to the list.

• Amino acid weights, IEPs
• some FASTA statistics one-liners
• quick overview of possible cli BLAST inputs/outputs (reading -help takes so long as they are all over the place)
• BLAST tabular output column names
• Karlin-Altschul formula
• definition of PAM and BLOSUM
• order of AAs in a substitution matrix/PSSM

List of most used file formats (.pdb, .bam, .fastq, etc etc), what information they contain, and what they can be used for? (and possibly the most well-known software(s) that reads them)

great idea!

a bit of biology:

the citrus cycle! http://student.ccbcmd.edu/~gkaiser/biotutorials/cellresp/images/u4fg35.jpg

or here you can find it also along other must-knows http://www.dummies.com/how-to/content/molecular-cell-biology-for-dummies-cheat-sheet.html

for R & Regex I already have seperate cheatsheets on my desk. One thing i am missing tough, is a cheatsheet for Regex, referring to in which environment one has to escape which characters and backreferences ( or $)

I like this question, so at the risk of sounding trite: my cheat sheet = a Google search. I store very little information these days; it's as quick and easy to search for it as and when required.

• No. seqs(fasta):

  grep \> file_name | wc -l

Biology by the numbers www.rpgroup.caltech.edu/publications/SnapShot2010.pdf

A useful addition would be a landscape or flowchart how to get from one file (format) into the next..... bioinformatics is about parsing it right....... :)