Molecular pathology: Difference between revisions

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| rarely done; follows karyotyping to better characterize unusual cases; can be thought of as a karyotype and a simultaneous ISH

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==Data formats==

Human gene naming is provided by the HUGO Gene Nomenclature Committee: https://www.genenames.org/

DNA data repositories

* NCBI: National Center for Biotechnology Information

**Standard sequencing data is usually located in Nucleotide database: https://www.ncbi.nlm.nih.gov/nuccore

**Next-gen sequencing data is in short read archive: https://www.ncbi.nlm.nih.gov/sra/docs/submit/

* EMBL: European Molecular Biology Laboratory

* DDBJ: DNA Data Bank of Japan

DNA sequence data formats

* GenBank: human readable, can be processed by computer (fixed width, first 10 characters are an identifier).

** NCBI Reference Sequence (RefSeq) project provides sequence records and related information.

** Prefix AC_ in acession number is for genomic data, NM_ is for mRNA.

* FASTA: Sequence information

** Header starts with > and is followed by a sequence ID.

** Sequence lines should wrap always at the same width.

** Lower-case letters may indicate repetitive regions.

* FASTQ: Current standard for sequencing data

** It is essentially FASTA with quality values for the sequence.

** Quality is on a scale from 0 - 40 and represented by a distinct character.

** Upper case letters ABCDEFGHI means high quality.

** Special letters !"#$%&'()*+,-. mean low quality.

==Polymerase chain reaction-based techniques==

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Line 204:

*[[DNA sequence comparison]].

*[[Tumour suppressor gene]].

*[[Next generation sequencing]].

==References==

@@ Line 119: / Line 119: @@
 | rarely done; follows karyotyping to better characterize unusual cases; can be thought of as a karyotype and a simultaneous ISH
 |}
+==Data formats==
+Human gene naming is provided by the HUGO Gene Nomenclature Committee: https://www.genenames.org/
+DNA data repositories
+* NCBI: National Center for Biotechnology Information
+**Standard sequencing data is usually located in Nucleotide database: https://www.ncbi.nlm.nih.gov/nuccore
+**Next-gen sequencing data is in short read archive: https://www.ncbi.nlm.nih.gov/sra/docs/submit/
+* EMBL: European Molecular Biology Laboratory
+* DDBJ: DNA Data Bank of Japan
+DNA sequence data formats
+* GenBank: human readable, can be processed by computer (fixed width, first 10 characters are an identifier).
+** NCBI Reference Sequence (RefSeq) project provides sequence records and related information.
+** Prefix AC_ in acession number is for genomic data, NM_ is for mRNA.
+* FASTA: Sequence information
+** Header starts with > and is followed by a sequence ID.
+** Sequence lines should wrap always at the same width.
+** Lower-case letters may indicate repetitive regions.
+* FASTQ: Current standard for sequencing data
+** It is essentially FASTA with quality values for the sequence.
+** Quality is on a scale from 0 - 40 and represented by a distinct character.
+** Upper case letters ABCDEFGHI means high quality.
+** Special letters !"#$%&'()*+,-. mean low quality.
 ==Polymerase chain reaction-based techniques==
@@ Line 179: / Line 204: @@
 *[[DNA sequence comparison]].
 *[[Tumour suppressor gene]].
+*[[Next generation sequencing]].
 ==References==

Molecular pathology: Difference between revisions

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