Bioinformatics/Subsequence: Difference between revisions

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 Write a routine to find all the positions of a randomly generated subsequence &nbsp; (four letters).
 <br><br>
+=={{header|Ada}}==
+<lang Ada>with Ada.Text_Io;
+with Ada.Strings.Fixed;
+with Ada.Numerics.Discrete_Random;
+procedure Sub_Sequence is
+   type Nucleotide is (A, C, G, T);
+   function To_Character (N : Nucleotide) return Character
+   is (case N is
+          when A => 'A', when C => 'C',
+          when G => 'G', when T => 'T');
+   package Random_Nucleotide is new Ada.Numerics.Discrete_Random (Nucleotide);
+   use Random_Nucleotide;
+   package Position_Io is new Ada.Text_Io.Integer_Io (Natural);
+   use Ada.Text_Io;
+   procedure Put_Bases (Seq : String; Width : Positive) is
+      First : Natural := Seq'First;
+   begin
+      while First < Seq'Last loop
+         declare
+            Last : constant Natural :=
+              Natural'Min (First + Width - 1, Seq'Last);
+         begin
+            Position_Io.Put (First); Put ("..");
+            Position_Io.Put (Last);  Put (" ");
+            Put (Seq (First .. Last));
+            New_Line;
+            First := Last + 1;
+         end;
+      end loop;
+   end Put_Bases;
+   Gen       : Generator;
+   Sequence  : String (1 .. 405);
+   Substring : String (1 ..   4);
+   Pos       : Natural := 0;
+begin
+   Position_Io.Default_Width := 3;
+   Reset (Gen);
+   Sequence  := (others => To_Character (Random (Gen)));
+   Substring := (others => To_Character (Random (Gen)));
+   Put_Line ("Search sequence:");
+   Put_Bases (Sequence, Width => 50);
+   New_Line;
+   Put ("Substring to search: ");
+   Put (Substring);
+   New_Line;
+   loop
+      Pos := Ada.Strings.Fixed.Index (Sequence, Substring, Pos + 1);
+      exit when Pos = 0;
+      Put ("Found at position: ");
+      Position_Io.Put (Pos); Put ("..");
+      Position_Io.Put (Pos + Substring'Length - 1);
+      New_Line;
+   end loop;
+end Sub_Sequence;</lang>
+{{out}}
+<pre>Search sequence:
+.. 50 CCTACGGAAAAGTGATAAGGACAGATACATAATCCTAAAACCCTGGAAAA
+..100 CTTGTCTCGCCAGAGTAGGGCTCGGCAGGGGGGGCAGTGTTTTAAAACGT
+..150 CAGAGAATAGGCTCTACCTTGTTAGACTGCGAGTACTGGAGCGTAGTTCC
+..200 TATATTGCAAGCTGCTACAGTAAGTATCAAAGTATGCCACACATCCTTCT
+..250 ACAACCGGATTGGTTGCCCAGTAGAAGGCTCGTAGTCACCGGACACGCTG
+..300 TTCTTAAGGTCGGTAAGCTATTACGTCCATGGGAGATTCTCAAGGGTGCG
+..350 TTAGCGGACCCCCGTTACGTCCACGTATCTTCCGTCCAACTACCCCCTAA
+..400 TGTCATTGACATCGCCCGAGTATTTAATTTATTTGAACGGCACCAATTTA
+..405 GAGCT
+Substring to search: TATT
+Found at position: 153..156
+Found at position: 269..272
+Found at position: 371..374
+Found at position: 380..383</pre>
 =={{header|Factor}}==