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%\usepackage{opensans}          % Can't make this work so far. Shame. Would be lovely.
\usepackage[normalem]{ulem}     % For underlining links
% Most of the following are not required for the majority
% of cheat sheets but are needed for some symbol support.
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\usepackage{MnSymbol}           % Symbols
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% Document Info
\author{disha2020}
\pdfinfo{
  /Title (ncbi.pdf)
  /Creator (Cheatography)
  /Author (disha2020)
  /Subject (NCBI Cheat Sheet)
}

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% Header and Footer
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\fancyhead[L]{
\noindent
\begin{multicols}{3}
\begin{tabulary}{5.8cm}{C}
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    \vspace{-7pt}
    {\parbox{\dimexpr\textwidth-2\fboxsep\relax}{\noindent
        \hspace*{-6pt}\includegraphics[width=5.8cm]{/web/www.cheatography.com/public/images/cheatography_logo.pdf}}
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\columnbreak
\begin{tabulary}{11cm}{L}
    \vspace{-2pt}\large{\bf{\textcolor{DarkBackground}{\textrm{NCBI Cheat Sheet}}}} \\
    \normalsize{by \textcolor{DarkBackground}{disha2020} via \textcolor{DarkBackground}{\uline{cheatography.com/147458/cs/32065/}}}
\end{tabulary}
\end{multicols}}

\fancyfoot[L]{ \footnotesize
\noindent
\begin{multicols}{3}
\begin{tabulary}{5.8cm}{LL}
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  \mymulticolumn{2}{p{5.377cm}}{\bf\textcolor{white}{Cheatographer}}  \\
  \vspace{-2pt}disha2020 \\
  \uline{cheatography.com/disha2020} \\
  \end{tabulary}
\vfill
\columnbreak
\begin{tabulary}{5.8cm}{L}
  \SetRowColor{FootBackground}
  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Cheat Sheet}}  \\
   \vspace{-2pt}Not Yet Published.\\
   Updated 11th May, 2022.\\
   Page {\thepage} of \pageref{LastPage}.
\end{tabulary}
\vfill
\columnbreak
\begin{tabulary}{5.8cm}{L}
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  \mymulticolumn{1}{p{5.377cm}}{\bf\textcolor{white}{Sponsor}}  \\
  \SetRowColor{white}
  \vspace{-5pt}
  %\includegraphics[width=48px,height=48px]{dave.jpeg}
  Measure your website readability!\\
  www.readability-score.com
\end{tabulary}
\end{multicols}}




\begin{document}
\raggedright
\raggedcolumns

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% from this page to resize cheat sheet text:
% www.emerson.emory.edu/services/latex/latex_169.html
\footnotesize % Small font.

\begin{multicols*}{2}

\begin{tabularx}{8.4cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{8.4cm}}{\bf\textcolor{white}{Restricted searches}}  \tn
% Row 0
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{formula: term{[}Field{]} sometimes also: "term"{[}Field{]}} \tn 
% Row Count 1 (+ 1)
% Row 1
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{horse{[}Organism{]}} \tn 
% Row Count 2 (+ 1)
% Row 2
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{neoplasms{[}MeSH Terms{]}} \tn 
% Row Count 3 (+ 1)
% Row 3
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{* {\emph{MeSH (Medical Subject Headings)}} \{\{link="https://meshb.nlm.nih.gov/search?searchMethod=FullWord\&searchInField=termDescriptor\&sort=\&size=20\&searchType=exactMatch\&q=neoplasms\&from=0"\}\}see here\{\{/link\}\}} \tn 
% Row Count 8 (+ 5)
% Row 4
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{prolactin{[}Protein Name{]}} \tn 
% Row Count 9 (+ 1)
% Row 5
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\mymulticolumn{1}{x{8.4cm}}{srcdb\_refseq{[}Properties{]}} \tn 
% Row Count 10 (+ 1)
% Row 6
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\mymulticolumn{1}{x{8.4cm}}{2010/06{[}Publication Date{]}} \tn 
% Row Count 11 (+ 1)
% Row 7
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{110:500{[}Sequence Length{]}} \tn 
% Row Count 12 (+ 1)
% Row 8
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{2015/3/1:2016/4/30{[}Publication Date{]}} \tn 
% Row Count 13 (+ 1)
% Row 9
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{NM\_002299.4{[}Accession{]}} \tn 
% Row Count 14 (+ 1)
% Row 10
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{equidae{[}All Fields{]}} \tn 
% Row Count 15 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{8.4cm}}{\bf\textcolor{white}{(Entrez) Searching options}}  \tn
% Row 0
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{\{\{link="https://www.ncbi.nlm.nih.gov/books/NBK3837/\#EntrezHelp.Entrez\_\%20Searching\_Options"\}\}Boolean operators:\{\{/link\}\}} \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{AND (default operator) - finds documents that include both terms (example: Homo sapience{[}Organism{]} AND BRCA1{[}Gene Name{]})} \tn 
% Row Count 6 (+ 3)
% Row 2
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{OR - finds related documentation to either of terms (example: hemoglobin{[}protein{]} OR haemoglobin{[}protein{]})} \tn 
% Row Count 9 (+ 3)
% Row 3
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{NOT - finds information related to the left terms, but not to the right (example: promoters OR response elements NOT human AND mammals)} \tn 
% Row Count 12 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{8.4cm}}{\bf\textcolor{white}{Truncation searching}}  \tn
% Row 0
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{NC\_0000*{[}Accession{]} AND Human{[}Organism{]}} \tn 
% Row Count 1 (+ 1)
% Row 1
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{{\emph{" * " allows to search for unfinished term}}} \tn 
% Row Count 2 (+ 1)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{8.4cm}}{\bf\textcolor{white}{SPLIGN}}  \tn
% Row 0
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{\{\{link="https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi"\}\}Splign\{\{/link\}\}- is a utility for computing cDNA-to-Genomic} \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{- identifies possible gene duplications} \tn 
% Row Count 4 (+ 1)
% Row 2
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{- recognizing introns, exones and splice signals} \tn 
% Row Count 5 (+ 1)
% Row 3
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\mymulticolumn{1}{x{8.4cm}}{{\emph{ * intrones - non-coding regions of an RNA transcript}}} \tn 
% Row Count 7 (+ 2)
% Row 4
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{{\emph{ * exone - coding regions of DNA}} \{\{link="https://www.youtube.com/watch?v=1UDTXDDzSrM"\}\}click here\{\{/link\}\}} \tn 
% Row Count 10 (+ 3)
% Row 5
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{Try SPLIGN \{\{link="https://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi?textpage=online\&level=form"\}\}here\{\{/link\}\}} \tn 
% Row Count 13 (+ 3)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{8.4cm}}{\bf\textcolor{white}{BLAST (Basic Local Alignment Search Tool)}}  \tn
% Row 0
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.} \tn 
% Row Count 4 (+ 4)
% Row 1
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.} \tn 
% Row Count 7 (+ 3)
% Row 2
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{Try BLAST \{\{link="https://blast.ncbi.nlm.nih.gov/Blast.cgi"\}\}here\{\{/link\}\}} \tn 
% Row Count 9 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{8.4cm}}{\bf\textcolor{white}{Conserved Domain Search}}  \tn
% Row 0
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{\{\{link="https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml"\}\}CD-Search\{\{/link\}\} is interface that searches through CDD (Conserved Domain Database) and returns an annotation of protein domains on the user query sequence} \tn 
% Row Count 5 (+ 5)
% Row 1
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{To compare two protein or nucleotide query, we can put them together in CD-Search. When results given we can check whether their domains have the same accession code.} \tn 
% Row Count 9 (+ 4)
% Row 2
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{Try CD-Search \{\{link="https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi"\}\}here\{\{/link\}\}} \tn 
% Row Count 11 (+ 2)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}

\begin{tabularx}{8.4cm}{X}
\SetRowColor{DarkBackground}
\mymulticolumn{1}{x{8.4cm}}{\bf\textcolor{white}{ORF finder}}  \tn
% Row 0
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{\{\{link="https://www.ncbi.nlm.nih.gov/orffinder/"\}\}ORF finder\{\{/link\}\}searches for open reading frames (ORFs) in the DNA sequence you enter.} \tn 
% Row Count 3 (+ 3)
% Row 1
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{* {\emph{open reading frames (ORFs) are defined as spans of DNA sequence between the start and stop codons (they include both introns and exons).}}} \tn 
% Row Count 6 (+ 3)
% Row 2
\SetRowColor{LightBackground}
\mymulticolumn{1}{x{8.4cm}}{The program returns the range of each ORF, along with its protein translation. Use ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP (there are buttons to head to these interfaces).} \tn 
% Row Count 12 (+ 6)
% Row 3
\SetRowColor{white}
\mymulticolumn{1}{x{8.4cm}}{The program returns the range of each ORF, along with its protein translation. Use ORF finder to search newly sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP (there are buttons to head to these interfaces).} \tn 
% Row Count 18 (+ 6)
\hhline{>{\arrayrulecolor{DarkBackground}}-}
\end{tabularx}
\par\addvspace{1.3em}


% That's all folks
\end{multicols*}

\end{document}